change in how numeric group definitions are handled in DTU and DGE compoarison. (59a65b9b) · Commits · github_fork / DTUrtle

R/dge_analysis.R

+3 −3

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		@@ -155,11 +155,11 @@ run_deseq2 <- function(counts, pd, id_col=NULL, cond_col, cond_levels=NULL, lfc_

		if(is.null(id_col)){
		assertthat::assert_that(all(rownames(pd) %in% colnames(counts)), msg = "Provided id_col does not match with sample names in counts.")
		samp <- data.frame("sample_id"=rownames(pd), "condition"=pd[[cond_col]],
		samp <- data.frame("sample_id"=rownames(pd), "condition"=as.character(pd[[cond_col]]),
		pd[,-c(which(colnames(pd)==cond_col)),drop=FALSE],
		row.names = NULL, stringsAsFactors = FALSE)
		}else{
		samp <- data.frame("sample_id"=pd[[id_col]], "condition"=pd[[cond_col]],
		samp <- data.frame("sample_id"=pd[[id_col]], "condition"=as.character(pd[[cond_col]]),
		pd[,-c(which(colnames(pd) %in% c(id_col, cond_col))),drop=FALSE],
		row.names = NULL, stringsAsFactors = FALSE)
		}
		@@ -243,7 +243,7 @@ run_deseq2 <- function(counts, pd, id_col=NULL, cond_col, cond_levels=NULL, lfc_
		dds <- do.call(DESeq2::DESeq, c(list("object"=dds), use_deseq_opts))

		#prepare LFC shrinking
		use_lfc_shrink_opts <- list("coef"=make.names(paste0("condition_",cond_levels[[1]],"_vs_",cond_levels[[2]])),
		use_lfc_shrink_opts <- list("coef"=paste0("condition_",make.names(cond_levels[[1]]),"_vs_",make.names(cond_levels[[2]])),
		"type"="apeglm",
		"svalue"=TRUE,
		"lfcThreshold"=lfc_threshold,

+2 −2

Original line number	Diff line number	Diff line
		@@ -339,11 +339,11 @@ run_drimseq <- function(counts, tx2gene, pd, id_col=NULL, cond_col, cond_levels=

		if(is.null(id_col)){
		assertthat::assert_that(all(rownames(pd) %in% colnames(counts)), msg = "Provided id_col does not match with sample names in counts.")
		samp <- data.frame("sample_id"=rownames(pd), "condition"=pd[[cond_col]],
		samp <- data.frame("sample_id"=rownames(pd), "condition"=as.character(pd[[cond_col]]),
		pd[,-c(which(colnames(pd)==cond_col)),drop=FALSE],
		row.names = NULL, stringsAsFactors = FALSE)
		}else{
		samp <- data.frame("sample_id"=pd[[id_col]], "condition"=pd[[cond_col]],
		samp <- data.frame("sample_id"=pd[[id_col]], "condition"=as.character(pd[[cond_col]]),
		pd[,-c(which(colnames(pd) %in% c(id_col, cond_col))),drop=FALSE],
		row.names = NULL, stringsAsFactors = FALSE)
		}

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		@@ -135,7 +135,7 @@
		<h1 data-toc-skip>Pre-processing of the Hoffman et al. human bulk RNA-seq data</h1>
		<h4 class="author">Tobias Tekath</h4>

		<h4 class="date">2021-07-04</h4>
		<h4 class="date">2021-07-09</h4>

		<small class="dont-index">Source: <a href="https://github.com/TobiTekath/DTUrtle/blob/master/vignettes/Hoffman_human_bulk_preprocess.Rmd"><code>vignettes/Hoffman_human_bulk_preprocess.Rmd</code></a></small>
		<div class="hidden name"><code>Hoffman_human_bulk_preprocess.Rmd</code></div>

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