Commit 33b07718 authored by Lena Hersemann's avatar Lena Hersemann

fixed count filter

parent c62c820b
......@@ -90,8 +90,9 @@ countMatrix = countData %>%
# Expression Filtering
genesBefore = nrow(countMatrix)
countMatrix %<>% filterByExpression(opts$min_count)
countMatrix %<>% filterByExpression(as.integer(opts$min_count))
genesAfter = nrow(countMatrix)
#' Counts were filtered to only retain genes which had more that `r opts$min_count` alignments in at least one replicate. This reduced the number of genes from `r genesBefore` to `r genesAfter`.
......@@ -449,7 +450,7 @@ summary(results(dds))
#deResults = alply(contrasts, 1, splat(function(sample_1, sample_2){
deResults = plyr::alply(contrasts, 1, plyr::splat(function(condition_1, condition_2){
#DEBUG sample_1=contrasts[1,1]; sample_2=contrasts[1,2]
#DEBUG condition_1=as_df(contrasts)[1,1]; condition_2=as_df(contrasts)[1,2]
# results(dds, contrast=c(contrastAttribute, sample_1, sample_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) %>%
......@@ -732,7 +733,7 @@ deAnnot = deResults %>% left_join(geneInfo)
write_tsv(deAnnot, path = paste0(resultsBase, "de_results.txt"))
#deAnnot = read_tsv(paste0(resultsBase, "de_results.txt"))
#' [deAnnot](`r paste0(resultsBase, "dba_results.txt")`)
#' [deAnnot](`r paste0(resultsBase, "de_results.txt")`)
## also export results which we'll always need for pathways overlays
deAnnot %>%
......
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