From 9ea07135f4d771241fb79e33d6ab20cc58f88828 Mon Sep 17 00:00:00 2001 From: Jakob Russel Date: Thu, 14 Feb 2019 15:58:16 +0100 Subject: [PATCH] update man --- man/allDA.Rd | 20 +++++++++++--------- man/powerDA.Rd | 2 +- man/runtimeDA.Rd | 2 +- man/testDA.Rd | 20 ++++++++++---------- 4 files changed, 23 insertions(+), 21 deletions(-) diff --git a/man/allDA.Rd b/man/allDA.Rd index 3547910..a7d8ace 100644 --- a/man/allDA.Rd +++ b/man/allDA.Rd @@ -4,17 +4,17 @@ \alias{allDA} \title{Run many differential abundance/expression methods} \usage{ -allDA(data, predictor, paired = NULL, covars = NULL, tests = c("neb", - "per", "adx", "sam", "qua", "fri", "znb", "zpo", "vli", "qpo", "poi", - "pea", "spe", "wil", "ttt", "ltt", "ltt2", "erq", "ere", "erq2", "ere2", - "msf", "zig", "ds2", "ds2x", "lim", "lli", "lli2", "aov", "lao", "lao2", - "kru", "lrm", "llm", "llm2", "tta", "ttc", "aoa", "aoc", "lma", "lmc", - "lia", "lic"), relative = TRUE, cores = (detectCores() - 1), +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), rng.seed = 123, p.adj = "fdr", args = list(), out.all = NULL, - alpha = 0.1, core.check = TRUE) + alpha = 0.1, core.check = TRUE, verbose = TRUE) } \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} +\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} \item{predictor}{The predictor of interest. Either a Factor or Numeric, OR if \code{data} is a \code{phyloseq} object the name of the variable in \code{sample_data(data)} in quotation. If the \code{predictor} is numeric it will be treated as such in the analyses} @@ -39,6 +39,8 @@ allDA(data, predictor, paired = NULL, covars = NULL, tests = c("neb", \item{alpha}{q-value threshold for calling significance. Default 0.1} \item{core.check}{If TRUE (default) will make an interactive check that the amount of cores specified are desired. Only if \code{cores>20}. This is to ensure that the function doesn't automatically overloads a server with workers.} + +\item{verbose}{If TRUE will print informative messages} } \value{ A list of results: @@ -54,5 +56,5 @@ A list of results: Run many differential abundance and expression tests at a time, to easily compare their results } \details{ -mva and bay are excluded by default, as they often are slow. +mva is excluded by default, as it is slow. } diff --git a/man/powerDA.Rd b/man/powerDA.Rd index 01ce87e..3072ecd 100644 --- a/man/powerDA.Rd +++ b/man/powerDA.Rd @@ -11,7 +11,7 @@ powerDA(data, predictor, paired = NULL, covars = NULL, test = NULL, out.all = NULL, core.check = TRUE, verbose = TRUE) } \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} +\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} \item{predictor}{The predictor of interest. Either a Factor or Numeric, OR if \code{data} is a \code{phyloseq} object the name of the variable in \code{sample_data(data)} in quotation. If the \code{predictor} is numeric it will be treated as such in the analyses} diff --git a/man/runtimeDA.Rd b/man/runtimeDA.Rd index 494327a..84ac6c2 100644 --- a/man/runtimeDA.Rd +++ b/man/runtimeDA.Rd @@ -10,7 +10,7 @@ runtimeDA(data, predictor, paired = NULL, covars = NULL, "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", "zpo", "znb", "adx", "ds2", "ds2x", "poi", "erq", "erq2"), + "bay", "per", "ds2", "ds2x", "zpo", "znb", "adx", "poi", "erq", "erq2"), cores = (detectCores() - 1), ...) } \arguments{ diff --git a/man/testDA.Rd b/man/testDA.Rd index 25f1226..68833a3 100644 --- a/man/testDA.Rd +++ b/man/testDA.Rd @@ -5,17 +5,17 @@ \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("neb", "per", "adx", "sam", "qua", "fri", "zpo", "znb", - "vli", "qpo", "poi", "pea", "wil", "ttt", "ltt", "ltt2", "erq", "erq2", - "ere", "ere2", "msf", "zig", "ds2", "ds2x", "lim", "lli", "lli2", "aov", - "lao", "lao2", "kru", "lrm", "llm", "llm2", "spe", "tta", "ttc", "aoa", - "aoc", "lma", "lmc", "lia", "lic"), relative = TRUE, effectSize = 5, - k = NULL, cores = (detectCores() - 1), rng.seed = 123, - p.adj = "fdr", args = list(), out.all = NULL, alpha = 0.1, - core.check = TRUE, verbose = TRUE) + 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), + rng.seed = 123, p.adj = "fdr", args = list(), out.all = NULL, + alpha = 0.1, core.check = TRUE, verbose = TRUE) } \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} +\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} \item{predictor}{The predictor of interest. Either a Factor or Numeric, OR if \code{data} is a \code{phyloseq} object the name of the variable in \code{sample_data(data)} in quotation. If the \code{predictor} is numeric it will be treated as such in the analyses} @@ -62,5 +62,5 @@ An object of class \code{DA}, which contains a list of results: Calculating Power, False Discovery Rates, False Positive Rates and AUC (Area Under the Receiver Operating Characteristic (ROC) Curve) for various differential abundance and expression methods } \details{ -mva and bay are excluded by default, as they often are slow. +mva is excluded by default, as it is slow. }