Nothing
createSummaryCounts <- function(counts, save_dir, prepend_str) {
## summarize nbreads per featurename
summary_counts <- list()
for (feature_name in names(counts$nbreads)) {
z <- list(counts$nbreads[[feature_name]])
names(z) <- paste(feature_name, "nbreads", sep="_")
summary_counts <- c(summary_counts , z)
}
## summarize nbfeatures per featurename
for (feature_name in names(counts$nbreads.byfeature)) {
z <- sum(counts$nbreads.byfeature[[feature_name]]>0)
names(z) <- paste(feature_name, "nbfeatures", sep="_")
summary_counts <- c(summary_counts , z)
}
## write file
df <- data.frame(name=names(summary_counts), value=unlist(summary_counts))
saveWithID(df, "summary_counts", id=prepend_str, save_dir=file.path(save_dir, "results"), format="tab")
}
mergeSummaryCounts <- function(dirs_to_merge, merged_dir, prepend_str, merge_nbfeatures) {
## load summary tables
lsummary_counts <- lapply(dirs_to_merge, function(dir) {
df <- getTabDataFromFile(dir, "summary_counts")
summary_counts <- as.numeric(df$value)
names(summary_counts) <- df$name
summary_counts
})
## merge nbreads by summing
summary_counts <- do.call(cbind, lsummary_counts)
summary_counts <- apply(summary_counts, 1, sum)
## use merge_nbfeatures to merge nbfeatures
summary_counts <- summary_counts[-grep("nbfeatures", names(summary_counts))]
summary_counts <- c(summary_counts, merge_nbfeatures)
## save merged summary table
df <- data.frame(name=names(summary_counts), value=unlist(summary_counts))
saveWithID(df, "summary_counts", id=prepend_str, save_dir=file.path(merged_dir, "results"), format="tab")
}
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