From 1a2c51335802ac90fb2430dda657e769ac2b683d Mon Sep 17 00:00:00 2001 From: Jakob Russel Date: Fri, 15 Mar 2019 11:26:49 +0100 Subject: [PATCH] 2.7.15 dont export interal functions, fix func name, no gitattributes --- .gitattributes | 1 - DESCRIPTION | 2 +- NAMESPACE | 5 ----- R/DA.adx.R | 2 +- R/DA.aoa.R | 2 +- R/DA.aoc.R | 2 +- R/DA.aov.R | 2 +- R/DA.bay.R | 2 +- R/DA.ds2.R | 2 +- R/DA.ds2x.R | 2 +- R/DA.ere.R | 2 +- R/DA.ere2.R | 2 +- R/DA.erq.R | 2 +- R/DA.erq2.R | 2 +- R/DA.fri.R | 2 +- R/DA.kru.R | 2 +- R/DA.lao.R | 2 +- R/DA.lao2.R | 2 +- R/DA.lia.R | 2 +- R/DA.lic.R | 2 +- R/DA.lim.R | 2 +- R/DA.lli.R | 2 +- R/DA.lli2.R | 2 +- R/DA.llm.R | 2 +- R/DA.llm2.R | 2 +- R/DA.lma.R | 2 +- R/DA.lmc.R | 2 +- R/DA.lrm.R | 2 +- R/DA.ltt.R | 2 +- R/DA.ltt2.R | 2 +- R/DA.msf.R | 2 +- R/DA.mva.R | 2 +- R/DA.neb.R | 2 +- R/DA.pea.R | 2 +- R/DA.per.R | 2 +- R/DA.phyloseq.R | 11 ----------- R/DA.poi.R | 2 +- R/DA.qpo.R | 2 +- R/DA.qua.R | 2 +- R/DA.sam.R | 2 +- R/DA.spe.R | 2 +- R/DA.tta.R | 2 +- R/DA.ttc.R | 2 +- R/DA.ttt.R | 2 +- R/DA.vli.R | 2 +- R/DA.wil.R | 2 +- R/DA.zig.R | 2 +- R/DA.znb.R | 2 +- R/DA.zpo.R | 2 +- R/DA.zzz.R | 2 +- R/add.tax.DA.R | 9 +-------- R/allDA.R | 6 +++--- R/norm.R | 6 ------ R/pruneTests.R | 15 +-------------- R/spikein.R | 16 ---------------- R/zzz.R | 2 +- man/DA.phyloseq.Rd | 23 ----------------------- man/add.tax.DA.Rd | 19 ------------------- man/gm_mean.Rd | 20 -------------------- man/pruneTests.Rd | 29 ----------------------------- man/spikein.Rd | 32 -------------------------------- 61 files changed, 53 insertions(+), 235 deletions(-) delete mode 100644 .gitattributes delete mode 100644 man/DA.phyloseq.Rd delete mode 100644 man/add.tax.DA.Rd delete mode 100644 man/gm_mean.Rd delete mode 100644 man/pruneTests.Rd delete mode 100644 man/spikein.Rd diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 00ed779..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -*.html linguist-vendored=true \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index f8da4f9..09d0c64 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: DAtest Title: Comparing Differential Abundance/Expression Methods -Version: 2.7.14 +Version: 2.7.15 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre")) diff --git a/NAMESPACE b/NAMESPACE index 87645cf..eb9d2b0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -41,7 +41,6 @@ export(DA.mva) export(DA.neb) export(DA.pea) export(DA.per) -export(DA.phyloseq) export(DA.poi) export(DA.qpo) export(DA.qua) @@ -56,17 +55,13 @@ export(DA.zig) export(DA.znb) export(DA.zpo) export(DA.zzz) -export(add.tax.DA) export(allDA) export(featurePlot) -export(gm_mean) export(norm_alr) export(norm_clr) export(powerDA) export(preDA) -export(pruneTests) export(runtimeDA) -export(spikein) export(testDA) export(vennDA) import(MASS) diff --git a/R/DA.adx.R b/R/DA.adx.R index 5e21b5f..1010a61 100644 --- a/R/DA.adx.R +++ b/R/DA.adx.R @@ -41,7 +41,7 @@ DA.adx <- function(data, predictor, ...){ x[!is.na(x$effect) & x$effect < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) x$Feature <- rownames(x) - if(class(data) == "phyloseq") x <- add.tax.DA(data, x) + if(class(data) == "phyloseq") x <- addTax(data, x) return(x) } else { diff --git a/R/DA.aoa.R b/R/DA.aoa.R index 2fc881b..2c89329 100644 --- a/R/DA.aoa.R +++ b/R/DA.aoa.R @@ -69,7 +69,7 @@ DA.aoa <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, all res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "ANOVA - ALR (aoa)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.aoc.R b/R/DA.aoc.R index 10b5f38..2d04396 100644 --- a/R/DA.aoc.R +++ b/R/DA.aoc.R @@ -67,7 +67,7 @@ DA.aoc <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, all res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "ANOVA - CLR (aoc)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.aov.R b/R/DA.aov.R index a2ca696..050a8ae 100644 --- a/R/DA.aov.R +++ b/R/DA.aov.R @@ -67,7 +67,7 @@ DA.aov <- function(data, predictor, covars = NULL, relative = TRUE, p.adj = "fdr res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "ANOVA (aov)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.bay.R b/R/DA.bay.R index a53561a..4dcb406 100644 --- a/R/DA.bay.R +++ b/R/DA.bay.R @@ -57,7 +57,7 @@ DA.bay <- function(data, predictor, allResults = FALSE, ...){ output_df$Method <- "baySeq (bay)" - if(class(data) == "phyloseq") output_df <- add.tax.DA(data, output_df) + if(class(data) == "phyloseq") output_df <- addTax(data, output_df) if(allResults) return(CD) else return(output_df) } else { diff --git a/R/DA.ds2.R b/R/DA.ds2.R index 3c93143..26a9ccc 100644 --- a/R/DA.ds2.R +++ b/R/DA.ds2.R @@ -126,7 +126,7 @@ DA.ds2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$Feature <- DESeq2::results(x)@rownames res$Method <- "DESeq2 man. geoMeans (ds2)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(x) else return(res) } else { diff --git a/R/DA.ds2x.R b/R/DA.ds2x.R index 8ce2316..ab1ace3 100644 --- a/R/DA.ds2x.R +++ b/R/DA.ds2x.R @@ -118,7 +118,7 @@ DA.ds2x <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL res$Feature <- DESeq2::results(x)@rownames res$Method <- "DESeq2 (ds2x)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(x) else return(res) } else { diff --git a/R/DA.ere.R b/R/DA.ere.R index 0e0fe4f..41e6404 100644 --- a/R/DA.ere.R +++ b/R/DA.ere.R @@ -59,7 +59,7 @@ DA.ere <- function(data, predictor, p.adj = "fdr", ...){ ta$Feature <- rownames(ta) ta$Method <- "EdgeR exact - TMM (ere)" - if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta) + if(class(data) == "phyloseq") ta <- addTax(data, ta) return(ta) diff --git a/R/DA.ere2.R b/R/DA.ere2.R index 33027c7..310e44b 100644 --- a/R/DA.ere2.R +++ b/R/DA.ere2.R @@ -58,7 +58,7 @@ DA.ere2 <- function(data, predictor, p.adj = "fdr", ...){ ta$Feature <- rownames(ta) ta$Method <- "EdgeR exact - RLE (ere2)" - if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta) + if(class(data) == "phyloseq") ta <- addTax(data, ta) return(ta) } else { diff --git a/R/DA.erq.R b/R/DA.erq.R index 608127a..30ee611 100644 --- a/R/DA.erq.R +++ b/R/DA.erq.R @@ -109,7 +109,7 @@ DA.erq <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL ta$Feature <- rownames(ta) ta$Method <- "EdgeR qll - TMM (erq)" - if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta) + if(class(data) == "phyloseq") ta <- addTax(data, ta) if(allResults) return(qlf) else return(ta) diff --git a/R/DA.erq2.R b/R/DA.erq2.R index 0fd4dc7..40b50b9 100644 --- a/R/DA.erq2.R +++ b/R/DA.erq2.R @@ -109,7 +109,7 @@ DA.erq2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL ta$Feature <- rownames(ta) ta$Method <- "EdgeR qll - RLE (erq2)" - if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta) + if(class(data) == "phyloseq") ta <- addTax(data, ta) if(allResults) return(qlf) else return(ta) diff --git a/R/DA.fri.R b/R/DA.fri.R index 9c9dd7f..aeebf0c 100644 --- a/R/DA.fri.R +++ b/R/DA.fri.R @@ -62,7 +62,7 @@ DA.fri <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr res$Feature <- gsub(".Friedman.*","",rownames(res)) res$Method <- "Friedman (fri)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.kru.R b/R/DA.kru.R index 42201ab..c86bf3e 100644 --- a/R/DA.kru.R +++ b/R/DA.kru.R @@ -54,7 +54,7 @@ DA.kru <- function(data, predictor, relative = TRUE, p.adj = "fdr", allResults = res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Kruskal-Wallis (kru)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.lao.R b/R/DA.lao.R index 8e60251..36604ff 100644 --- a/R/DA.lao.R +++ b/R/DA.lao.R @@ -65,7 +65,7 @@ DA.lao <- function(data, predictor, covars = NULL, relative = TRUE, p.adj = "fdr res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Log ANOVA (lao)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.lao2.R b/R/DA.lao2.R index 698e282..a19ae3e 100644 --- a/R/DA.lao2.R +++ b/R/DA.lao2.R @@ -64,7 +64,7 @@ DA.lao2 <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 0.001 res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Log ANOVA 2 (lao2)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.lia.R b/R/DA.lia.R index cd08260..b27355d 100644 --- a/R/DA.lia.R +++ b/R/DA.lia.R @@ -104,7 +104,7 @@ DA.lia <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$Feature <- rownames(res) res$Method <- "LIMMA - ALR (lia)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.lic.R b/R/DA.lic.R index 0cb1447..68c45db 100644 --- a/R/DA.lic.R +++ b/R/DA.lic.R @@ -104,7 +104,7 @@ DA.lic <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$Feature <- rownames(res) res$Method <- "LIMMA - CLR (lic)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.lim.R b/R/DA.lim.R index 213d2b6..667528a 100644 --- a/R/DA.lim.R +++ b/R/DA.lim.R @@ -105,7 +105,7 @@ DA.lim <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$Feature <- rownames(res) res$Method <- "LIMMA (lim)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.lli.R b/R/DA.lli.R index 67f363f..f03414d 100644 --- a/R/DA.lli.R +++ b/R/DA.lli.R @@ -103,7 +103,7 @@ DA.lli <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$Feature <- rownames(res) res$Method <- "Log LIMMA (lli)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.lli2.R b/R/DA.lli2.R index b9d5d64..7ab7acd 100644 --- a/R/DA.lli2.R +++ b/R/DA.lli2.R @@ -103,7 +103,7 @@ DA.lli2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL res$Feature <- rownames(res) res$Method <- "Log LIMMA 2 (lli2)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.llm.R b/R/DA.llm.R index ddc0948..a5429a0 100644 --- a/R/DA.llm.R +++ b/R/DA.llm.R @@ -156,7 +156,7 @@ DA.llm <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Log Linear reg. (llm)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.llm2.R b/R/DA.llm2.R index 04ac672..46d37ef 100644 --- a/R/DA.llm2.R +++ b/R/DA.llm2.R @@ -155,7 +155,7 @@ DA.llm2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Log Linear reg. 2 (llm2)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.lma.R b/R/DA.lma.R index 7d3ccc6..9c532f0 100644 --- a/R/DA.lma.R +++ b/R/DA.lma.R @@ -159,7 +159,7 @@ DA.lma <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Linear model - ALR (lma)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.lmc.R b/R/DA.lmc.R index 48d19db..5fa797b 100644 --- a/R/DA.lmc.R +++ b/R/DA.lmc.R @@ -158,7 +158,7 @@ DA.lmc <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Linear model - CLR (lmc)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.lrm.R b/R/DA.lrm.R index d751a49..a36bf01 100644 --- a/R/DA.lrm.R +++ b/R/DA.lrm.R @@ -154,7 +154,7 @@ DA.lrm <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$pval.adj <- p.adjust(res$pval, method = p.adj) res$Feature <- rownames(res) res$Method <- "Linear regression (lrm)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.ltt.R b/R/DA.ltt.R index 6f60b26..156e293 100644 --- a/R/DA.ltt.R +++ b/R/DA.ltt.R @@ -82,7 +82,7 @@ DA.ltt <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "Log t-test (ltt)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.ltt2.R b/R/DA.ltt2.R index 87d72ff..bb8f53d 100644 --- a/R/DA.ltt2.R +++ b/R/DA.ltt2.R @@ -81,7 +81,7 @@ DA.ltt2 <- function(data, predictor, paired = NULL, p.adj = "fdr", delta = 0.001 res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "Log t-test2 (ltt2)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.msf.R b/R/DA.msf.R index 0436536..50b004e 100644 --- a/R/DA.msf.R +++ b/R/DA.msf.R @@ -61,7 +61,7 @@ DA.msf <- function(data, predictor, p.adj = "fdr", allResults = FALSE, ...){ temp_table[!is.na(temp_table$logFC) & temp_table$logFC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) temp_table$Method <- "MgSeq Feature (msf)" - if(class(data) == "phyloseq") temp_table <- add.tax.DA(data, temp_table) + if(class(data) == "phyloseq") temp_table <- addTax(data, temp_table) if(allResults) return(mgsfit) else return(temp_table) diff --git a/R/DA.mva.R b/R/DA.mva.R index 99fb6bd..42a09ac 100644 --- a/R/DA.mva.R +++ b/R/DA.mva.R @@ -105,7 +105,7 @@ DA.mva <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$Feature <- rownames(pvals.unadj$uni.test) res$Method <- "mvabund (mva)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.neb.R b/R/DA.neb.R index 21394df..5f98dde 100644 --- a/R/DA.neb.R +++ b/R/DA.neb.R @@ -211,7 +211,7 @@ DA.neb <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$Method <- "Negbinom GLM (neb)" if(nrow(res) > 1){ - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) } return(res) } else { diff --git a/R/DA.pea.R b/R/DA.pea.R index fad496e..56f310c 100644 --- a/R/DA.pea.R +++ b/R/DA.pea.R @@ -54,7 +54,7 @@ DA.pea <- function(data, predictor, relative = TRUE, p.adj = "fdr", ...){ res$Method <- "Pearson (pea)" # Add tax table if available - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.per.R b/R/DA.per.R index 1cdb8ac..d3c908b 100644 --- a/R/DA.per.R +++ b/R/DA.per.R @@ -125,7 +125,7 @@ DA.per <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr output_df$pval.adj <- p.adjust(output_df$pval, method = p.adj) output_df$Method <- "Permutation (per)" - if(class(data) == "phyloseq") output_df <- add.tax.DA(data, output_df) + if(class(data) == "phyloseq") output_df <- addTax(data, output_df) return(output_df) } diff --git a/R/DA.phyloseq.R b/R/DA.phyloseq.R index c9d4062..622bb8e 100644 --- a/R/DA.phyloseq.R +++ b/R/DA.phyloseq.R @@ -1,14 +1,3 @@ -#' Extract data from a \code{phyloseq} object to be used in \code{DAtest} -#' -#' Internal function -#' -#' @param data A \code{phyloseq} object -#' @param predictor The \code{predictor} of interest -#' @param paired Factor for paired/blocked experimental designs. -#' @param covars A character vector with names of the variables in \code{sample_data(data)} -#' @return A list with data extracted from the \code{phyloseq} object -#' @export - DA.phyloseq <- function(data, predictor, paired = NULL, covars = NULL){ ok <- tryCatch({ diff --git a/R/DA.poi.R b/R/DA.poi.R index 72f4767..d0c078c 100644 --- a/R/DA.poi.R +++ b/R/DA.poi.R @@ -245,7 +245,7 @@ DA.poi <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU res$Method <- "Poisson GLM (poi)" if(nrow(res) > 1){ - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) } return(res) } diff --git a/R/DA.qpo.R b/R/DA.qpo.R index 7054e6e..6f2c145 100644 --- a/R/DA.qpo.R +++ b/R/DA.qpo.R @@ -158,7 +158,7 @@ DA.qpo <- function(data, predictor, covars = NULL, relative = TRUE, out.all = NU res$Method <- "Quasi-Poisson GLM (qpo)" if(nrow(res) > 1){ - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) } return(res) } diff --git a/R/DA.qua.R b/R/DA.qua.R index 944a306..de1c2a6 100644 --- a/R/DA.qua.R +++ b/R/DA.qua.R @@ -64,7 +64,7 @@ DA.qua <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr res$Feature <- gsub(".Quade.*","",rownames(res)) res$Method <- "Quade (qua)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.sam.R b/R/DA.sam.R index ba5f7c5..eac5021 100644 --- a/R/DA.sam.R +++ b/R/DA.sam.R @@ -99,7 +99,7 @@ DA.sam <- function(data, predictor, paired = NULL, fdr.output = 0.05, allResults df$Method <- "SAMseq (sam)" - if(class(data) == "phyloseq") df <- add.tax.DA(data, df) + if(class(data) == "phyloseq") df <- addTax(data, df) if(allResults){ return(res) diff --git a/R/DA.spe.R b/R/DA.spe.R index e1e0137..8ca2bca 100644 --- a/R/DA.spe.R +++ b/R/DA.spe.R @@ -51,7 +51,7 @@ DA.spe <- function(data, predictor, relative = TRUE, p.adj = "fdr", ...){ res$Feature <- rownames(res) res$Method <- "Spearman (spe)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.tta.R b/R/DA.tta.R index 4a25efc..dca71c4 100644 --- a/R/DA.tta.R +++ b/R/DA.tta.R @@ -86,7 +86,7 @@ DA.tta <- function(data, predictor, paired = NULL, p.adj = "fdr", delta = 1, tes res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "t-test - ALR (tta)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.ttc.R b/R/DA.ttc.R index 39d6ca5..8114265 100644 --- a/R/DA.ttc.R +++ b/R/DA.ttc.R @@ -84,7 +84,7 @@ DA.ttc <- function(data, predictor, paired = NULL, p.adj = "fdr", delta = 1, tes res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "t-test - CLR (ttc)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } diff --git a/R/DA.ttt.R b/R/DA.ttt.R index e925091..1b8a45b 100644 --- a/R/DA.ttt.R +++ b/R/DA.ttt.R @@ -84,7 +84,7 @@ DA.ttt <- function(data, predictor,paired = NULL, relative = TRUE, p.adj = "fdr" res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "t-test (ttt)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } } \ No newline at end of file diff --git a/R/DA.vli.R b/R/DA.vli.R index 72f1e30..0c021a1 100644 --- a/R/DA.vli.R +++ b/R/DA.vli.R @@ -108,7 +108,7 @@ DA.vli <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL res$Feature <- rownames(res) res$Method <- "LIMMA voom (vli)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) if(allResults) return(fit.eb) else return(res) diff --git a/R/DA.wil.R b/R/DA.wil.R index 9832f58..2335230 100644 --- a/R/DA.wil.R +++ b/R/DA.wil.R @@ -84,7 +84,7 @@ DA.wil <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2]) res$Feature <- rownames(res) res$Method <- "Wilcox (wil)" - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/DA.zig.R b/R/DA.zig.R index 4da9a50..c3a3bc4 100644 --- a/R/DA.zig.R +++ b/R/DA.zig.R @@ -94,7 +94,7 @@ DA.zig <- function(data, predictor, paired = NULL, covars = NULL, p.adj = "fdr", temp_table$Feature <- rownames(temp_table) temp_table$Method <- "MgSeq ZIG (zig)" - if(class(data) == "phyloseq") temp_table <- add.tax.DA(data, temp_table) + if(class(data) == "phyloseq") temp_table <- addTax(data, temp_table) if(allResults) return(mgsfit) else return(temp_table) diff --git a/R/DA.znb.R b/R/DA.znb.R index a1d5758..d5cf197 100644 --- a/R/DA.znb.R +++ b/R/DA.znb.R @@ -167,7 +167,7 @@ DA.znb <- function(data, predictor, covars = NULL, relative = TRUE, out.all = NU res$Method <- "ZI-NegBin GLM (znb)" if(nrow(res) > 1){ - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) } return(res) } diff --git a/R/DA.zpo.R b/R/DA.zpo.R index 146dd24..e8c21bf 100644 --- a/R/DA.zpo.R +++ b/R/DA.zpo.R @@ -166,7 +166,7 @@ DA.zpo <- function(data, predictor, covars = NULL, relative = TRUE, out.all = NU res$Method <- "ZI-Poisson GLM (zpo)" if(nrow(res) > 1){ - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) } return(res) } diff --git a/R/DA.zzz.R b/R/DA.zzz.R index 6927e1b..55d78c1 100644 --- a/R/DA.zzz.R +++ b/R/DA.zzz.R @@ -69,7 +69,7 @@ DA.zzz <- function(data, predictor, paired = NULL, covars = NULL, p.adj = "fdr", if(!all(c("pval","Feature","Method") %in% colnames(res))) stop("The following columns has to be present in output: pval, Feature and Method") res$pval.adj <- p.adjust(res$pval, method = p.adj) - if(class(data) == "phyloseq") res <- add.tax.DA(data, res) + if(class(data) == "phyloseq") res <- addTax(data, res) return(res) } diff --git a/R/add.tax.DA.R b/R/add.tax.DA.R index 320a5d5..909f6c5 100644 --- a/R/add.tax.DA.R +++ b/R/add.tax.DA.R @@ -1,11 +1,4 @@ -#' Add tax_table from phyloseq object -#' -#' Internal function -#' @param data phyloseq object -#' @param res data.frame with results -#' @return \code{res} merged with the tax.table from the phyloseq object -#' @export -add.tax.DA <- function(data, res){ +addTax <- function(data, res){ loadNamespace("phyloseq") diff --git a/R/allDA.R b/R/allDA.R index fa825fe..18ec2c4 100644 --- a/R/allDA.R +++ b/R/allDA.R @@ -284,7 +284,7 @@ allDA <- function(data, predictor, paired = NULL, covars = NULL, if(length(Pval.raw) > 0){ df.raw <- suppressWarnings(Reduce(function(x,y) merge(x, y, by= "Feature", all.x = TRUE, all.y = TRUE), Pval.raw)) colnames(df.raw)[2:ncol(df.raw)] <- names(Pval.raw) - if(class(data) == "phyloseq") df.raw <- add.tax.DA(data, df.raw) + if(class(data) == "phyloseq") df.raw <- addTax(data, df.raw) } else { df.raw <- NULL } @@ -307,7 +307,7 @@ allDA <- function(data, predictor, paired = NULL, covars = NULL, } colnames(df.adj)[ncol(df.adj)] <- "sam" } - if(class(data) == "phyloseq") df.adj <- add.tax.DA(data, df.adj) + if(class(data) == "phyloseq") df.adj <- addTax(data, df.adj) } else { df.adj <- NULL } @@ -364,7 +364,7 @@ allDA <- function(data, predictor, paired = NULL, covars = NULL, list.est <- list.est[!sapply(list.est, is.null)] if(length(list.est) > 0){ df.est <- Reduce(function(x,y) merge(x, y, by= "Feature", all.x = TRUE, all.y = TRUE), list.est) - if(class(data) == "phyloseq") df.est <- add.tax.DA(data, df.est) + if(class(data) == "phyloseq") df.est <- addTax(data, df.est) } else { df.est <- NULL } diff --git a/R/norm.R b/R/norm.R index bdbefa5..083ea75 100644 --- a/R/norm.R +++ b/R/norm.R @@ -1,9 +1,3 @@ -#' Geometric means -#' -#' @param x numeric vector -#' @return The geometric mean -#' @examples gm_mean(1:10) -#' @export gm_mean = function(x){ if(any(x < 0, na.rm = TRUE)){ stop("Negative values not allowed") diff --git a/R/pruneTests.R b/R/pruneTests.R index 16ba65d..2ec784d 100644 --- a/R/pruneTests.R +++ b/R/pruneTests.R @@ -1,15 +1,3 @@ -#' Prune tests argument for \code{testDA} -#' -#' @param tests A character vector with names of tests -#' @param predictor Vector with predictor variable -#' @param paired Factor with paired variable -#' @param covars Named list with covariables -#' @param relative Include tests that work with relative abundances (TRUE) or only absolute abundances (FALSE) -#' @param decimal Exclude tests that do not work with decimals (TRUE) -#' @param zeroes If FALSE will exclude tests that include zero-inflation -#' @return A character with the tests argument pruned according to the parameters -#' @export - pruneTests <- function(tests, predictor, paired, covars, relative, decimal, zeroes){ # Prune test argument if packages are not installed @@ -19,8 +7,7 @@ pruneTests <- function(tests, predictor, paired, covars, relative, decimal, zero if(!"metagenomeSeq" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("msf","zig")] if(!"DESeq2" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("ds2","ds2x")] if(!"limma" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("lim","lli","lli2","vli","lia","lic")] - if(!"statmod" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("lim","lli","lli2","vli","lia","lic")] - if(!"RAIDA" %in% rownames(installed.packages())) tests <- tests[tests != "rai"] + if(!"statmod" %in% rownames(installed.packages()) && is.null(paired)) tests <- tests[!tests %in% c("lim","lli","lli2","vli","lia","lic")] if(!"pscl" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("zpo","znb")] if(!"samr" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("sam")] if(!"mvabund" %in% rownames(installed.packages())) tests <- tests[!tests %in% c("mva")] diff --git a/R/spikein.R b/R/spikein.R index ca9b4a7..c36ac27 100644 --- a/R/spikein.R +++ b/R/spikein.R @@ -1,19 +1,3 @@ -#' Spike-in -#' -#' Internal function for the \code{testDA} function. -#' -#' Modified version of the one from: -#' https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0208-8. -#' -#' @param count_table Matrix or data.frame. Table with taxa/genes/proteins as rows and samples as columns -#' @param predictor Factor or Numeric. The predictor of interest. E.g. case and control. If the \code{predictor} has more than two levels, only the 2. level will be spiked. -#' @param effectSize Integer. The effect size for the spike-ins. Default 2 -#' @param k Vector of length 3. Number of Features to spike in each tertile (lower, mid, upper). k=c(5,10,15): 5 features spiked in low abundance tertile, 10 features spiked in mid abundance tertile and 15 features spiked in high abundance tertile. Default c(5,5,5) -#' @param num.pred Logical. Is the \code{predictor} numeric? Default FALSE -#' @param relative Logical. Are abundances relative? Default TRUE -#' @return Returns a list where the first element is the count_table with the spiked features, and the second element contains rownames of the spiked features. -#' @export - spikein <- function(count_table, predictor, effectSize = 2, k, num.pred = FALSE, relative = TRUE){ if(effectSize < 0) stop("Effect size should be positive") diff --git a/R/zzz.R b/R/zzz.R index fe4ff23..f6b9958 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,3 +1,3 @@ .onAttach <- function(libname, pkgname){ - packageStartupMessage("DAtest version 2.7.14") + packageStartupMessage("DAtest version 2.7.15") } \ No newline at end of file diff --git a/man/DA.phyloseq.Rd b/man/DA.phyloseq.Rd deleted file mode 100644 index 579398a..0000000 --- a/man/DA.phyloseq.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/DA.phyloseq.R -\name{DA.phyloseq} -\alias{DA.phyloseq} -\title{Extract data from a \code{phyloseq} object to be used in \code{DAtest}} -\usage{ -DA.phyloseq(data, predictor, paired = NULL, covars = NULL) -} -\arguments{ -\item{data}{A \code{phyloseq} object} - -\item{predictor}{The \code{predictor} of interest} - -\item{paired}{Factor for paired/blocked experimental designs.} - -\item{covars}{A character vector with names of the variables in \code{sample_data(data)}} -} -\value{ -A list with data extracted from the \code{phyloseq} object -} -\description{ -Internal function -} diff --git a/man/add.tax.DA.Rd b/man/add.tax.DA.Rd deleted file mode 100644 index a2ff32b..0000000 --- a/man/add.tax.DA.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/add.tax.DA.R -\name{add.tax.DA} -\alias{add.tax.DA} -\title{Add tax_table from phyloseq object} -\usage{ -add.tax.DA(data, res) -} -\arguments{ -\item{data}{phyloseq object} - -\item{res}{data.frame with results} -} -\value{ -\code{res} merged with the tax.table from the phyloseq object -} -\description{ -Internal function -} diff --git a/man/gm_mean.Rd b/man/gm_mean.Rd deleted file mode 100644 index c9c1c06..0000000 --- a/man/gm_mean.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/norm.R -\name{gm_mean} -\alias{gm_mean} -\title{Geometric means} -\usage{ -gm_mean(x) -} -\arguments{ -\item{x}{numeric vector} -} -\value{ -The geometric mean -} -\description{ -Geometric means -} -\examples{ -gm_mean(1:10) -} diff --git a/man/pruneTests.Rd b/man/pruneTests.Rd deleted file mode 100644 index 5cca0bd..0000000 --- a/man/pruneTests.Rd +++ /dev/null @@ -1,29 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/pruneTests.R -\name{pruneTests} -\alias{pruneTests} -\title{Prune tests argument for \code{testDA}} -\usage{ -pruneTests(tests, predictor, paired, covars, relative, decimal, zeroes) -} -\arguments{ -\item{tests}{A character vector with names of tests} - -\item{predictor}{Vector with predictor variable} - -\item{paired}{Factor with paired variable} - -\item{covars}{Named list with covariables} - -\item{relative}{Include tests that work with relative abundances (TRUE) or only absolute abundances (FALSE)} - -\item{decimal}{Exclude tests that do not work with decimals (TRUE)} - -\item{zeroes}{If FALSE will exclude tests that include zero-inflation} -} -\value{ -A character with the tests argument pruned according to the parameters -} -\description{ -Prune tests argument for \code{testDA} -} diff --git a/man/spikein.Rd b/man/spikein.Rd deleted file mode 100644 index 499b8cb..0000000 --- a/man/spikein.Rd +++ /dev/null @@ -1,32 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/spikein.R -\name{spikein} -\alias{spikein} -\title{Spike-in} -\usage{ -spikein(count_table, predictor, effectSize = 2, k, num.pred = FALSE, - relative = TRUE) -} -\arguments{ -\item{count_table}{Matrix or data.frame. Table with taxa/genes/proteins as rows and samples as columns} - -\item{predictor}{Factor or Numeric. The predictor of interest. E.g. case and control. If the \code{predictor} has more than two levels, only the 2. level will be spiked.} - -\item{effectSize}{Integer. The effect size for the spike-ins. Default 2} - -\item{k}{Vector of length 3. Number of Features to spike in each tertile (lower, mid, upper). k=c(5,10,15): 5 features spiked in low abundance tertile, 10 features spiked in mid abundance tertile and 15 features spiked in high abundance tertile. Default c(5,5,5)} - -\item{num.pred}{Logical. Is the \code{predictor} numeric? Default FALSE} - -\item{relative}{Logical. Are abundances relative? Default TRUE} -} -\value{ -Returns a list where the first element is the count_table with the spiked features, and the second element contains rownames of the spiked features. -} -\description{ -Internal function for the \code{testDA} function. -} -\details{ -Modified version of the one from: -https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0208-8. -}