From 146217bd1ea742ca9ad64ad19bf0c29b9aa6019c Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Thu, 14 Nov 2024 10:47:00 -0500 Subject: [PATCH 1/2] fix example data --- inst/templates/rnaseq/DE/DEG.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/templates/rnaseq/DE/DEG.Rmd b/inst/templates/rnaseq/DE/DEG.Rmd index 9f02750..727ae18 100644 --- a/inst/templates/rnaseq/DE/DEG.Rmd +++ b/inst/templates/rnaseq/DE/DEG.Rmd @@ -393,8 +393,8 @@ names(contrasts)=names_to_use de_list=lapply(contrasts, function(contrast){ resLFC = results(de, contrast=contrast) coef = paste0(contrast[1], "_", contrast[2], "_vs_", contrast[3]) - resLFCS <- lfcShrink(de, coef=coef, type="apeglm") - # resLFCS <- lfcShrink(de, contrast=contrast, type="ash") + #resLFCS <- lfcShrink(de, coef=coef, type="apeglm") + resLFCS <- lfcShrink(de, contrast=contrast, type="ash") res <- as.data.frame(resLFCS) %>% rownames_to_column('gene_id') %>% left_join(rdata, by = 'gene_id') %>% From 59502c7e8d62578c7abe5daa55d7aa705ff92b2f Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Thu, 14 Nov 2024 10:48:01 -0500 Subject: [PATCH 2/2] fix linting --- inst/templates/rnaseq/DE/DEG.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/templates/rnaseq/DE/DEG.Rmd b/inst/templates/rnaseq/DE/DEG.Rmd index 727ae18..220d531 100644 --- a/inst/templates/rnaseq/DE/DEG.Rmd +++ b/inst/templates/rnaseq/DE/DEG.Rmd @@ -393,7 +393,7 @@ names(contrasts)=names_to_use de_list=lapply(contrasts, function(contrast){ resLFC = results(de, contrast=contrast) coef = paste0(contrast[1], "_", contrast[2], "_vs_", contrast[3]) - #resLFCS <- lfcShrink(de, coef=coef, type="apeglm") + # resLFCS <- lfcShrink(de, coef=coef, type="apeglm") resLFCS <- lfcShrink(de, contrast=contrast, type="ash") res <- as.data.frame(resLFCS) %>%