Commit 0c52bb1f authored by Lena Hersemann's avatar Lena Hersemann

changed the independent filtering method in the DESeq2 results() function from...

changed the independent filtering method in the DESeq2 results() function from the default to independent hypothesis weighting (IHW)
parent 71039e60
......@@ -56,6 +56,7 @@ library(knitr)
#biocLite("DESeq2")
library(DESeq2)
#load_pack(readr)
library(IHW)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
......@@ -464,8 +465,8 @@ summary(results(dds))
deResults = plyr::alply(contrasts, 1, plyr::splat(function(condition_1, condition_2){
#DEBUG condition_1=as_df(contrasts)[1,1]; condition_2=as_df(contrasts)[1,2]
# results(dds, contrast=c(contrastAttribute, condition_1, condition_2)) %>%
# results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff, filterFun = ihw) %>%
results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff) %>%
results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff, filterFun = ihw) %>%
# results(dds, contrast = c(contrastAttribute, condition_1, condition_2), lfcThreshold = lfc_cutoff) %>%
as_tibble() %>%
tibble::rownames_to_column("ensembl_gene_id") %>%
## see http://rpackages.ianhowson.com/bioc/DESeq2/man/results.html when using contrasts argument
......
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