From a3de6a0f7e400112e20b94ee76fb4e253cc04181 Mon Sep 17 00:00:00 2001 From: Jakob Russel Date: Wed, 24 Jun 2020 16:19:51 +0200 Subject: [PATCH] v2.7.16 - Fix problem with parallel on macOS in R4.0 #13. Man pages rebuild with new roxygen --- DESCRIPTION | 4 ++-- R/zzz.R | 6 +++++- man/DA.aoa.Rd | 11 +++++++++-- man/DA.aoc.Rd | 11 +++++++++-- man/DA.aov.Rd | 11 +++++++++-- man/DA.ds2.Rd | 14 ++++++++++++-- man/DA.ds2x.Rd | 15 ++++++++++++--- man/DA.erq.Rd | 13 +++++++++++-- man/DA.erq2.Rd | 14 +++++++++++--- man/DA.fri.Rd | 11 +++++++++-- man/DA.kru.Rd | 10 ++++++++-- man/DA.lao.Rd | 12 ++++++++++-- man/DA.lao2.Rd | 11 +++++++++-- man/DA.lia.Rd | 14 ++++++++++++-- man/DA.lic.Rd | 14 ++++++++++++-- man/DA.lim.Rd | 15 ++++++++++++--- man/DA.lli.Rd | 16 +++++++++++++--- man/DA.lli2.Rd | 15 ++++++++++++--- man/DA.llm.Rd | 16 +++++++++++++--- man/DA.llm2.Rd | 15 ++++++++++++--- man/DA.lma.Rd | 14 ++++++++++++-- man/DA.lmc.Rd | 14 ++++++++++++-- man/DA.lrm.Rd | 15 ++++++++++++--- man/DA.lsmeans.Rd | 10 ++++++++-- man/DA.ltt.Rd | 19 ++++++++++++++----- man/DA.ltt2.Rd | 18 +++++++++++++----- man/DA.mva.Rd | 16 +++++++++++++--- man/DA.neb.Rd | 16 +++++++++++++--- man/DA.per.Rd | 16 +++++++++++----- man/DA.poi.Rd | 16 +++++++++++++--- man/DA.qpo.Rd | 15 ++++++++++++--- man/DA.qua.Rd | 11 +++++++++-- man/DA.sam.Rd | 10 ++++++++-- man/DA.tta.Rd | 11 +++++++++-- man/DA.ttc.Rd | 11 +++++++++-- man/DA.ttt.Rd | 18 +++++++++++++----- man/DA.vli.Rd | 13 +++++++++++-- man/DA.wil.Rd | 18 +++++++++++++----- man/DA.zig.Rd | 13 +++++++++++-- man/DA.znb.Rd | 15 ++++++++++++--- man/DA.zpo.Rd | 15 ++++++++++++--- man/DA.zzz.Rd | 10 ++++++++-- man/allDA.Rd | 26 ++++++++++++++++++-------- man/featurePlot.Rd | 14 +++++++++++--- man/powerDA.Rd | 24 +++++++++++++++++++----- man/runtimeDA.Rd | 23 +++++++++++++++-------- man/summary.DA.Rd | 11 +++++++++-- man/testDA.Rd | 30 +++++++++++++++++++++--------- man/vennDA.Rd | 11 +++++++++-- 49 files changed, 552 insertions(+), 149 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 09d0c64..923589d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: DAtest Title: Comparing Differential Abundance/Expression Methods -Version: 2.7.15 +Version: 2.7.16 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre")) @@ -49,5 +49,5 @@ Suggests: lsmeans, License: GPL (>= 3) | file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.0 BugReports: https://github.com/Russel88/DAtest/issues diff --git a/R/zzz.R b/R/zzz.R index f6b9958..30f7054 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,3 +1,7 @@ .onAttach <- function(libname, pkgname){ - packageStartupMessage("DAtest version 2.7.15") + packageStartupMessage("DAtest version 2.7.16") + if (Sys.getenv("RSTUDIO") == "1" && !nzchar(Sys.getenv("RSTUDIO_TERM")) && + Sys.info()["sysname"] == "Darwin" && getRversion() == "4.0.0") { + snow::setDefaultClusterOptions(setup_strategy = "sequential") + } } \ No newline at end of file diff --git a/man/DA.aoa.Rd b/man/DA.aoa.Rd index 792684d..ccd9092 100644 --- a/man/DA.aoa.Rd +++ b/man/DA.aoa.Rd @@ -4,8 +4,15 @@ \alias{DA.aoa} \title{ANOVA - Multiplicative zero-correction and additive log-ratio normalization.} \usage{ -DA.aoa(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, - allResults = FALSE, ...) +DA.aoa( + data, + predictor, + covars = NULL, + p.adj = "fdr", + delta = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.aoc.Rd b/man/DA.aoc.Rd index 459a6fa..f686019 100644 --- a/man/DA.aoc.Rd +++ b/man/DA.aoc.Rd @@ -4,8 +4,15 @@ \alias{DA.aoc} \title{ANOVA - Multiplicative zero-correction and additive log-ratio normalization.} \usage{ -DA.aoc(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, - allResults = FALSE, ...) +DA.aoc( + data, + predictor, + covars = NULL, + p.adj = "fdr", + delta = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.aov.Rd b/man/DA.aov.Rd index dc39203..396bf2d 100644 --- a/man/DA.aov.Rd +++ b/man/DA.aov.Rd @@ -4,8 +4,15 @@ \alias{DA.aov} \title{ANOVA} \usage{ -DA.aov(data, predictor, covars = NULL, relative = TRUE, - p.adj = "fdr", allResults = FALSE, ...) +DA.aov( + data, + predictor, + covars = NULL, + relative = TRUE, + p.adj = "fdr", + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.ds2.Rd b/man/DA.ds2.Rd index b207da0..1400bde 100644 --- a/man/DA.ds2.Rd +++ b/man/DA.ds2.Rd @@ -4,8 +4,18 @@ \alias{DA.ds2} \title{DESeq2 with manual geometric means} \usage{ -DA.ds2(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", coeff = 2, coeff.ref = 1, allResults = FALSE, ...) +DA.ds2( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.ds2x.Rd b/man/DA.ds2x.Rd index 38e0d9a..eb21920 100644 --- a/man/DA.ds2x.Rd +++ b/man/DA.ds2x.Rd @@ -4,9 +4,18 @@ \alias{DA.ds2x} \title{DESeq2} \usage{ -DA.ds2x(data, predictor, paired = NULL, covars = NULL, - out.all = NULL, p.adj = "fdr", coeff = 2, coeff.ref = 1, - allResults = FALSE, ...) +DA.ds2x( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.erq.Rd b/man/DA.erq.Rd index b4cc46e..8cf1d19 100644 --- a/man/DA.erq.Rd +++ b/man/DA.erq.Rd @@ -4,8 +4,17 @@ \alias{DA.erq} \title{EdgeR quasi-likelihood - TMM normalization} \usage{ -DA.erq(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", coeff = 2, allResults = FALSE, ...) +DA.erq( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.erq2.Rd b/man/DA.erq2.Rd index d04a2b3..5c6c829 100644 --- a/man/DA.erq2.Rd +++ b/man/DA.erq2.Rd @@ -4,9 +4,17 @@ \alias{DA.erq2} \title{EdgeR quasi-likelihood - RLE normalization} \usage{ -DA.erq2(data, predictor, paired = NULL, covars = NULL, - out.all = NULL, p.adj = "fdr", coeff = 2, allResults = FALSE, - ...) +DA.erq2( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.fri.Rd b/man/DA.fri.Rd index bc2569f..3bddf22 100644 --- a/man/DA.fri.Rd +++ b/man/DA.fri.Rd @@ -4,8 +4,15 @@ \alias{DA.fri} \title{Friedman Rank Sum test} \usage{ -DA.fri(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", allResults = FALSE, ...) +DA.fri( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.kru.Rd b/man/DA.kru.Rd index 6a11b77..6463fca 100644 --- a/man/DA.kru.Rd +++ b/man/DA.kru.Rd @@ -4,8 +4,14 @@ \alias{DA.kru} \title{Kruskal-Wallis test} \usage{ -DA.kru(data, predictor, relative = TRUE, p.adj = "fdr", - allResults = FALSE, ...) +DA.kru( + data, + predictor, + relative = TRUE, + p.adj = "fdr", + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lao.Rd b/man/DA.lao.Rd index fd40033..e9be23c 100644 --- a/man/DA.lao.Rd +++ b/man/DA.lao.Rd @@ -4,8 +4,16 @@ \alias{DA.lao} \title{ANOVA} \usage{ -DA.lao(data, predictor, covars = NULL, relative = TRUE, - p.adj = "fdr", delta = 1, allResults = FALSE, ...) +DA.lao( + data, + predictor, + covars = NULL, + relative = TRUE, + p.adj = "fdr", + delta = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lao2.Rd b/man/DA.lao2.Rd index a4018c5..b2396ca 100644 --- a/man/DA.lao2.Rd +++ b/man/DA.lao2.Rd @@ -4,8 +4,15 @@ \alias{DA.lao2} \title{ANOVA} \usage{ -DA.lao2(data, predictor, covars = NULL, p.adj = "fdr", delta = 0.001, - allResults = FALSE, ...) +DA.lao2( + data, + predictor, + covars = NULL, + p.adj = "fdr", + delta = 0.001, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lia.Rd b/man/DA.lia.Rd index a207ad1..892e844 100644 --- a/man/DA.lia.Rd +++ b/man/DA.lia.Rd @@ -4,8 +4,18 @@ \alias{DA.lia} \title{LIMMA - Multiplicative zero-correction and additive log-ratio normalization.} \usage{ -DA.lia(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", delta = 1, coeff = 2, allResults = FALSE, ...) +DA.lia( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lic.Rd b/man/DA.lic.Rd index 8c09dc3..ef213ef 100644 --- a/man/DA.lic.Rd +++ b/man/DA.lic.Rd @@ -4,8 +4,18 @@ \alias{DA.lic} \title{LIMMA - Multiplicative zero-correction and center log-ratio normalization.} \usage{ -DA.lic(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", delta = 1, coeff = 2, allResults = FALSE, ...) +DA.lic( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lim.Rd b/man/DA.lim.Rd index 96c29e9..c4181d1 100644 --- a/man/DA.lim.Rd +++ b/man/DA.lim.Rd @@ -4,9 +4,18 @@ \alias{DA.lim} \title{LIMMA} \usage{ -DA.lim(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", coeff = 2, - allResults = FALSE, ...) +DA.lim( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lli.Rd b/man/DA.lli.Rd index cf74828..b47d49b 100644 --- a/man/DA.lli.Rd +++ b/man/DA.lli.Rd @@ -4,9 +4,19 @@ \alias{DA.lli} \title{LIMMA} \usage{ -DA.lli(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", delta = 1, - coeff = 2, allResults = FALSE, ...) +DA.lli( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lli2.Rd b/man/DA.lli2.Rd index 09ea5c0..d39d7e6 100644 --- a/man/DA.lli2.Rd +++ b/man/DA.lli2.Rd @@ -4,9 +4,18 @@ \alias{DA.lli2} \title{LIMMA} \usage{ -DA.lli2(data, predictor, paired = NULL, covars = NULL, - out.all = NULL, p.adj = "fdr", delta = 0.001, coeff = 2, - allResults = FALSE, ...) +DA.lli2( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 0.001, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.llm.Rd b/man/DA.llm.Rd index 598b8d1..62003b7 100644 --- a/man/DA.llm.Rd +++ b/man/DA.llm.Rd @@ -4,9 +4,19 @@ \alias{DA.llm} \title{Log linear regression} \usage{ -DA.llm(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", delta = 1, - coeff = 2, allResults = FALSE, ...) +DA.llm( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.llm2.Rd b/man/DA.llm2.Rd index 71eab2f..aab1471 100644 --- a/man/DA.llm2.Rd +++ b/man/DA.llm2.Rd @@ -4,9 +4,18 @@ \alias{DA.llm2} \title{Log linear regression} \usage{ -DA.llm2(data, predictor, paired = NULL, covars = NULL, - out.all = NULL, p.adj = "fdr", delta = 0.001, coeff = 2, - allResults = FALSE, ...) +DA.llm2( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 0.001, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lma.Rd b/man/DA.lma.Rd index ddf14c3..7f9f2cf 100644 --- a/man/DA.lma.Rd +++ b/man/DA.lma.Rd @@ -4,8 +4,18 @@ \alias{DA.lma} \title{Linear regression - Multiplicative zero-correction and additive log-ratio normalization.} \usage{ -DA.lma(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", delta = 1, coeff = 2, allResults = FALSE, ...) +DA.lma( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lmc.Rd b/man/DA.lmc.Rd index ac5c1b8..9a823cb 100644 --- a/man/DA.lmc.Rd +++ b/man/DA.lmc.Rd @@ -4,8 +4,18 @@ \alias{DA.lmc} \title{Linear regression - Multiplicative zero-correction and center log-ratio normalization.} \usage{ -DA.lmc(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", delta = 1, coeff = 2, allResults = FALSE, ...) +DA.lmc( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + delta = 1, + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lrm.Rd b/man/DA.lrm.Rd index c8550ee..b6f53e2 100644 --- a/man/DA.lrm.Rd +++ b/man/DA.lrm.Rd @@ -4,9 +4,18 @@ \alias{DA.lrm} \title{Linear regression} \usage{ -DA.lrm(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", coeff = 2, - allResults = FALSE, ...) +DA.lrm( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.lsmeans.Rd b/man/DA.lsmeans.Rd index 2d870aa..740940a 100644 --- a/man/DA.lsmeans.Rd +++ b/man/DA.lsmeans.Rd @@ -4,8 +4,14 @@ \alias{DA.lsmeans} \title{Run \code{lsmeans} on all features from \code{DAtest} results with \code{allResults = TRUE}} \usage{ -DA.lsmeans(results, variable = "predictor", predictor = NULL, - covars = NULL, p.adj = "fdr", ...) +DA.lsmeans( + results, + variable = "predictor", + predictor = NULL, + covars = NULL, + p.adj = "fdr", + ... +) } \arguments{ \item{results}{Output from a \code{DA."test"} function with \code{allResults = TRUE}} diff --git a/man/DA.ltt.Rd b/man/DA.ltt.Rd index 8735b40..0cc1d8a 100644 --- a/man/DA.ltt.Rd +++ b/man/DA.ltt.Rd @@ -4,11 +4,20 @@ \alias{DA.ltt} \title{Welch t-test} \usage{ -DA.ltt(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", delta = 1, testStat = function(case, control) { - log2((mean(case) + 0.001)/(mean(control) + 0.001)) }, - testStat.pair = function(case, control) { log2(mean((case + - 0.001)/(control + 0.001))) }, allResults = FALSE, ...) +DA.ltt( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + delta = 1, + testStat = function(case, control) { log2((mean(case) + 0.001)/(mean(control) + + 0.001)) }, + testStat.pair = function(case, control) { log2(mean((case + 0.001)/(control + + 0.001))) }, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.ltt2.Rd b/man/DA.ltt2.Rd index 65ddae1..fe7aeed 100644 --- a/man/DA.ltt2.Rd +++ b/man/DA.ltt2.Rd @@ -4,11 +4,19 @@ \alias{DA.ltt2} \title{Welch t-test} \usage{ -DA.ltt2(data, predictor, paired = NULL, p.adj = "fdr", delta = 0.001, - testStat = function(case, control) { - log2((mean(exp(case)))/(mean(exp(control)))) }, - testStat.pair = function(case, control) { - log2(mean((exp(case))/(exp(control)))) }, allResults = FALSE, ...) +DA.ltt2( + data, + predictor, + paired = NULL, + p.adj = "fdr", + delta = 0.001, + testStat = function(case, control) { log2((mean(exp(case)))/(mean(exp(control)))) + }, + testStat.pair = function(case, control) { log2(mean((exp(case))/(exp(control)))) + }, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.mva.Rd b/man/DA.mva.Rd index 7204a7d..d9d127a 100644 --- a/man/DA.mva.Rd +++ b/man/DA.mva.Rd @@ -4,9 +4,19 @@ \alias{DA.mva} \title{Mvabund} \usage{ -DA.mva(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, p.adj = "fdr", coeff = 2, coeff.ref = 1, - resamp = "montecarlo", allResults = FALSE, ...) +DA.mva( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + resamp = "montecarlo", + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.neb.Rd b/man/DA.neb.Rd index f742c1d..d24734b 100644 --- a/man/DA.neb.Rd +++ b/man/DA.neb.Rd @@ -4,9 +4,19 @@ \alias{DA.neb} \title{Negative binomial glm} \usage{ -DA.neb(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", coeff = 2, - coeff.ref = 1, allResults = FALSE, ...) +DA.neb( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.per.Rd b/man/DA.per.Rd index b73b1ae..6da1044 100644 --- a/man/DA.per.Rd +++ b/man/DA.per.Rd @@ -4,11 +4,17 @@ \alias{DA.per} \title{Permutation test of user-defined test statistic} \usage{ -DA.per(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", testStat = function(case, control) { - log2((mean(case) + 1)/(mean(control) + 1)) }, - testStat.pair = function(case, control) { log2(mean((case + - 1)/(control + 1))) }, noOfIterations = 10000, margin = 50) +DA.per( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + testStat = function(case, control) { log2((mean(case) + 1)/(mean(control) + 1)) }, + testStat.pair = function(case, control) { log2(mean((case + 1)/(control + 1))) }, + noOfIterations = 10000, + margin = 50 +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.poi.Rd b/man/DA.poi.Rd index 7580b9b..ef9f350 100644 --- a/man/DA.poi.Rd +++ b/man/DA.poi.Rd @@ -4,9 +4,19 @@ \alias{DA.poi} \title{Poisson glm} \usage{ -DA.poi(data, predictor, paired = NULL, covars = NULL, - relative = TRUE, out.all = NULL, p.adj = "fdr", coeff = 2, - coeff.ref = 1, allResults = FALSE, ...) +DA.poi( + data, + predictor, + paired = NULL, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.qpo.Rd b/man/DA.qpo.Rd index 32cbab3..58737ed 100644 --- a/man/DA.qpo.Rd +++ b/man/DA.qpo.Rd @@ -4,9 +4,18 @@ \alias{DA.qpo} \title{Quasi-poisson glm} \usage{ -DA.qpo(data, predictor, covars = NULL, relative = TRUE, - out.all = NULL, p.adj = "fdr", coeff = 2, coeff.ref = 1, - allResults = FALSE, ...) +DA.qpo( + data, + predictor, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.qua.Rd b/man/DA.qua.Rd index a78c131..772d882 100644 --- a/man/DA.qua.Rd +++ b/man/DA.qua.Rd @@ -4,8 +4,15 @@ \alias{DA.qua} \title{Quade test} \usage{ -DA.qua(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", allResults = FALSE, ...) +DA.qua( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.sam.Rd b/man/DA.sam.Rd index b28e0bf..69d12e9 100644 --- a/man/DA.sam.Rd +++ b/man/DA.sam.Rd @@ -4,8 +4,14 @@ \alias{DA.sam} \title{SAMSeq} \usage{ -DA.sam(data, predictor, paired = NULL, fdr.output = 0.05, - allResults = FALSE, ...) +DA.sam( + data, + predictor, + paired = NULL, + fdr.output = 0.05, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.tta.Rd b/man/DA.tta.Rd index be208a1..737cb02 100644 --- a/man/DA.tta.Rd +++ b/man/DA.tta.Rd @@ -4,10 +4,17 @@ \alias{DA.tta} \title{Welch t-test - Multiplicative zero-correction and additive log-ratio normalization.} \usage{ -DA.tta(data, predictor, paired = NULL, p.adj = "fdr", delta = 1, +DA.tta( + data, + predictor, + paired = NULL, + p.adj = "fdr", + delta = 1, testStat = function(case, control) { mean(case) - mean(control) }, testStat.pair = function(case, control) { mean(case - control) }, - allResults = FALSE, ...) + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.ttc.Rd b/man/DA.ttc.Rd index b7fe048..0ad7c75 100644 --- a/man/DA.ttc.Rd +++ b/man/DA.ttc.Rd @@ -4,10 +4,17 @@ \alias{DA.ttc} \title{Welch t-test - Multiplicative zero-correction and center log-ratio normalization.} \usage{ -DA.ttc(data, predictor, paired = NULL, p.adj = "fdr", delta = 1, +DA.ttc( + data, + predictor, + paired = NULL, + p.adj = "fdr", + delta = 1, testStat = function(case, control) { mean(case) - mean(control) }, testStat.pair = function(case, control) { mean(case - control) }, - allResults = FALSE, ...) + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.ttt.Rd b/man/DA.ttt.Rd index c26fd44..1765184 100644 --- a/man/DA.ttt.Rd +++ b/man/DA.ttt.Rd @@ -4,11 +4,19 @@ \alias{DA.ttt} \title{Welch t-test} \usage{ -DA.ttt(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", testStat = function(case, control) { - log2((mean(case) + 0.001)/(mean(control) + 0.001)) }, - testStat.pair = function(case, control) { log2(mean((case + - 0.001)/(control + 0.001))) }, allResults = FALSE, ...) +DA.ttt( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + testStat = function(case, control) { log2((mean(case) + 0.001)/(mean(control) + + 0.001)) }, + testStat.pair = function(case, control) { log2(mean((case + 0.001)/(control + + 0.001))) }, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.vli.Rd b/man/DA.vli.Rd index 74234f3..1d9bc31 100644 --- a/man/DA.vli.Rd +++ b/man/DA.vli.Rd @@ -4,8 +4,17 @@ \alias{DA.vli} \title{LIMMA with \code{voom}} \usage{ -DA.vli(data, predictor, paired = NULL, covars = NULL, out.all = NULL, - p.adj = "fdr", coeff = 2, allResults = FALSE, ...) +DA.vli( + data, + predictor, + paired = NULL, + covars = NULL, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.wil.Rd b/man/DA.wil.Rd index 9ea2e55..8e81607 100644 --- a/man/DA.wil.Rd +++ b/man/DA.wil.Rd @@ -4,11 +4,19 @@ \alias{DA.wil} \title{Wilcoxon Rank Sum and Signed Rank Test} \usage{ -DA.wil(data, predictor, paired = NULL, relative = TRUE, - p.adj = "fdr", testStat = function(case, control) { - log2((mean(case) + 0.001)/(mean(control) + 0.001)) }, - testStat.pair = function(case, control) { log2(mean((case + - 0.001)/(control + 0.001))) }, allResults = FALSE, ...) +DA.wil( + data, + predictor, + paired = NULL, + relative = TRUE, + p.adj = "fdr", + testStat = function(case, control) { log2((mean(case) + 0.001)/(mean(control) + + 0.001)) }, + testStat.pair = function(case, control) { log2(mean((case + 0.001)/(control + + 0.001))) }, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.zig.Rd b/man/DA.zig.Rd index 5ca8623..3c7c431 100644 --- a/man/DA.zig.Rd +++ b/man/DA.zig.Rd @@ -4,8 +4,17 @@ \alias{DA.zig} \title{MetagenomeSeq ZIG} \usage{ -DA.zig(data, predictor, paired = NULL, covars = NULL, p.adj = "fdr", - by = 2, eff = 0.5, allResults = FALSE, ...) +DA.zig( + data, + predictor, + paired = NULL, + covars = NULL, + p.adj = "fdr", + by = 2, + eff = 0.5, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.znb.Rd b/man/DA.znb.Rd index 90c126f..51a8df1 100644 --- a/man/DA.znb.Rd +++ b/man/DA.znb.Rd @@ -4,9 +4,18 @@ \alias{DA.znb} \title{Zero inflated Negative Binomial glm} \usage{ -DA.znb(data, predictor, covars = NULL, relative = TRUE, - out.all = NULL, p.adj = "fdr", coeff = 2, coeff.ref = 1, - allResults = FALSE, ...) +DA.znb( + data, + predictor, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.zpo.Rd b/man/DA.zpo.Rd index 8c3e3e6..d46990e 100644 --- a/man/DA.zpo.Rd +++ b/man/DA.zpo.Rd @@ -4,9 +4,18 @@ \alias{DA.zpo} \title{Zero inflated Poisson glm} \usage{ -DA.zpo(data, predictor, covars = NULL, relative = TRUE, - out.all = NULL, p.adj = "fdr", coeff = 2, coeff.ref = 1, - allResults = FALSE, ...) +DA.zpo( + data, + predictor, + covars = NULL, + relative = TRUE, + out.all = NULL, + p.adj = "fdr", + coeff = 2, + coeff.ref = 1, + allResults = FALSE, + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/DA.zzz.Rd b/man/DA.zzz.Rd index 045e53a..2e8577d 100644 --- a/man/DA.zzz.Rd +++ b/man/DA.zzz.Rd @@ -4,8 +4,14 @@ \alias{DA.zzz} \title{User-defined function} \usage{ -DA.zzz(data, predictor, paired = NULL, covars = NULL, p.adj = "fdr", - FUN = NULL) +DA.zzz( + data, + predictor, + paired = NULL, + covars = NULL, + p.adj = "fdr", + FUN = NULL +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples} diff --git a/man/allDA.Rd b/man/allDA.Rd index 3823b9a..68da20d 100644 --- a/man/allDA.Rd +++ b/man/allDA.Rd @@ -4,14 +4,24 @@ \alias{allDA} \title{Run many differential abundance/expression methods} \usage{ -allDA(data, predictor, paired = NULL, covars = NULL, tests = c("bay", - "ds2", "ds2x", "per", "adx", "znb", "zpo", "msf", "zig", "erq", "erq2", - "neb", "qpo", "poi", "sam", "lrm", "llm", "llm2", "lma", "lmc", "ere", - "ere2", "pea", "spe", "wil", "kru", "qua", "fri", "ttt", "ltt", "ltt2", - "tta", "ttc", "aov", "lao", "lao2", "aoa", "aoc", "vli", "lim", "lli", - "lli2", "lia", "lic"), relative = TRUE, cores = (detectCores() - 1), - p.adj = "fdr", args = list(), out.all = NULL, alpha = 0.1, - core.check = TRUE, verbose = TRUE) +allDA( + data, + predictor, + paired = NULL, + covars = NULL, + tests = c("bay", "ds2", "ds2x", "per", "adx", "znb", "zpo", "msf", "zig", "erq", + "erq2", "neb", "qpo", "poi", "sam", "lrm", "llm", "llm2", "lma", "lmc", "ere", + "ere2", "pea", "spe", "wil", "kru", "qua", "fri", "ttt", "ltt", "ltt2", "tta", "ttc", + "aov", "lao", "lao2", "aoa", "aoc", "vli", "lim", "lli", "lli2", "lia", "lic"), + relative = TRUE, + cores = (detectCores() - 1), + p.adj = "fdr", + args = list(), + out.all = NULL, + alpha = 0.1, + core.check = TRUE, + verbose = TRUE +) } \arguments{ \item{data}{Either a data.frame with counts/abundances, OR a \code{phyloseq} object. If a data.frame is provided rows should be taxa/genes/proteins and columns samples, and there should be rownames} diff --git a/man/featurePlot.Rd b/man/featurePlot.Rd index d4bd41f..68eaa48 100644 --- a/man/featurePlot.Rd +++ b/man/featurePlot.Rd @@ -4,9 +4,17 @@ \alias{featurePlot} \title{Plot association between abundance of a feature and predictor} \usage{ -featurePlot(data, predictor, paired = NULL, covars = NULL, - feature = NULL, relative = TRUE, logScale = FALSE, delta = 0.001, - covar.quant = c(0, 1/3, 2/3, 1)) +featurePlot( + data, + predictor, + paired = NULL, + covars = NULL, + feature = NULL, + relative = TRUE, + logScale = FALSE, + delta = 0.001, + covar.quant = c(0, 1/3, 2/3, 1) +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples, and there should be rownames} diff --git a/man/powerDA.Rd b/man/powerDA.Rd index d15d103..efc3ad9 100644 --- a/man/powerDA.Rd +++ b/man/powerDA.Rd @@ -4,11 +4,25 @@ \alias{powerDA} \title{Estimating (empirical) statistical power} \usage{ -powerDA(data, predictor, paired = NULL, covars = NULL, test = NULL, - effectSizes = c(2, 4, 8, 16, 32), alpha.p = 0.05, alpha.q = 0.1, - p.adj = "fdr", R = 5, relative = TRUE, k = NULL, - cores = (detectCores() - 1), args = list(), out.all = NULL, - core.check = TRUE, verbose = TRUE) +powerDA( + data, + predictor, + paired = NULL, + covars = NULL, + test = NULL, + effectSizes = c(2, 4, 8, 16, 32), + alpha.p = 0.05, + alpha.q = 0.1, + p.adj = "fdr", + R = 5, + relative = TRUE, + k = NULL, + cores = (detectCores() - 1), + args = list(), + out.all = NULL, + core.check = TRUE, + verbose = TRUE +) } \arguments{ \item{data}{Either a data.frame with counts/abundances, OR a \code{phyloseq} object. If a data.frame is provided rows should be taxa/genes/proteins and columns samples, and there should be rownames} diff --git a/man/runtimeDA.Rd b/man/runtimeDA.Rd index 686a772..c53e81b 100644 --- a/man/runtimeDA.Rd +++ b/man/runtimeDA.Rd @@ -4,14 +4,21 @@ \alias{runtimeDA} \title{Estimate runtime of \code{testDA} on large datasets} \usage{ -runtimeDA(data, predictor, paired = NULL, covars = NULL, - subsamples = c(500, 1000, 1500, 2000), subsamples.slow = c(100, 150, - 200, 250), tests = c("sam", "qua", "fri", "vli", "qpo", "pea", "wil", - "ttt", "ltt", "ltt2", "ere", "ere2", "msf", "zig", "lim", "lli", "lli2", - "aov", "lao", "lao2", "kru", "lrm", "llm", "llm2", "spe", "aoa", "aoc", - "tta", "ttc", "lma", "lmc", "lia", "lic"), tests.slow = c("mva", "neb", - "bay", "per", "ds2", "ds2x", "zpo", "znb", "adx", "poi", "erq", "erq2"), - cores = (detectCores() - 1), ...) +runtimeDA( + data, + predictor, + paired = NULL, + covars = NULL, + subsamples = c(500, 1000, 1500, 2000), + subsamples.slow = c(100, 150, 200, 250), + tests = c("sam", "qua", "fri", "vli", "qpo", "pea", "wil", "ttt", "ltt", "ltt2", + "ere", "ere2", "msf", "zig", "lim", "lli", "lli2", "aov", "lao", "lao2", "kru", + "lrm", "llm", "llm2", "spe", "aoa", "aoc", "tta", "ttc", "lma", "lmc", "lia", "lic"), + tests.slow = c("mva", "neb", "bay", "per", "ds2", "ds2x", "zpo", "znb", "adx", "poi", + "erq", "erq2"), + cores = (detectCores() - 1), + ... +) } \arguments{ \item{data}{Either a matrix with counts/abundances, OR a \code{phyloseq} object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples, and there should be rownames} diff --git a/man/summary.DA.Rd b/man/summary.DA.Rd index 0c5496c..4830fc5 100644 --- a/man/summary.DA.Rd +++ b/man/summary.DA.Rd @@ -4,8 +4,15 @@ \alias{summary.DA} \title{Summary of results from \code{testDA}} \usage{ -\method{summary}{DA}(object, sort = "Score", boot = TRUE, - prob = c(0.05, 0.95), N = 1000, decimals = 2, ...) +\method{summary}{DA}( + object, + sort = "Score", + boot = TRUE, + prob = c(0.05, 0.95), + N = 1000, + decimals = 2, + ... +) } \arguments{ \item{object}{The output from the \code{testDA} function} diff --git a/man/testDA.Rd b/man/testDA.Rd index 16714ef..fb7473b 100644 --- a/man/testDA.Rd +++ b/man/testDA.Rd @@ -4,15 +4,27 @@ \alias{testDA} \title{Comparing differential abundance/expression methods by Empirical power and False Discovery Rate} \usage{ -testDA(data, predictor, paired = NULL, covars = NULL, R = 20, - tests = c("bay", "ds2", "ds2x", "per", "adx", "znb", "zpo", "msf", - "zig", "erq", "erq2", "neb", "qpo", "poi", "sam", "lrm", "llm", "llm2", - "lma", "lmc", "ere", "ere2", "pea", "spe", "wil", "kru", "qua", "fri", - "ttt", "ltt", "ltt2", "tta", "ttc", "aov", "lao", "lao2", "aoa", "aoc", - "vli", "lim", "lli", "lli2", "lia", "lic"), relative = TRUE, - effectSize = 5, k = NULL, cores = (detectCores() - 1), - p.adj = "fdr", args = list(), out.all = NULL, alpha = 0.1, - core.check = TRUE, verbose = TRUE) +testDA( + data, + predictor, + paired = NULL, + covars = NULL, + R = 20, + tests = c("bay", "ds2", "ds2x", "per", "adx", "znb", "zpo", "msf", "zig", "erq", + "erq2", "neb", "qpo", "poi", "sam", "lrm", "llm", "llm2", "lma", "lmc", "ere", + "ere2", "pea", "spe", "wil", "kru", "qua", "fri", "ttt", "ltt", "ltt2", "tta", "ttc", + "aov", "lao", "lao2", "aoa", "aoc", "vli", "lim", "lli", "lli2", "lia", "lic"), + relative = TRUE, + effectSize = 5, + k = NULL, + cores = (detectCores() - 1), + p.adj = "fdr", + args = list(), + out.all = NULL, + alpha = 0.1, + core.check = TRUE, + verbose = TRUE +) } \arguments{ \item{data}{Either a data.frame with counts/abundances, OR a \code{phyloseq} object. If a data.frame is provided rows should be taxa/genes/proteins and columns samples, and there should be rownames} diff --git a/man/vennDA.Rd b/man/vennDA.Rd index a0ae003..91d05fb 100644 --- a/man/vennDA.Rd +++ b/man/vennDA.Rd @@ -4,8 +4,15 @@ \alias{vennDA} \title{Plot Venn diagram from \code{allDA} object} \usage{ -vennDA(x, tests = NULL, alpha = 0.1, split = FALSE, output = FALSE, - pkg = "eulerr", ...) +vennDA( + x, + tests = NULL, + alpha = 0.1, + split = FALSE, + output = FALSE, + pkg = "eulerr", + ... +) } \arguments{ \item{x}{(Required) Output from the \code{allDA} function}