Description Usage Arguments Details Value Author(s) Examples
View source: R/count_summaries.R
Given a list of featureCounts summary files, return a dataframe of read counts broken down by type (assigned, unassigned due to multimapping, etc)
1 | count_summaries(inFiles, verbose = TRUE)
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inFiles |
Character - List of featureCounts output files |
verbose |
Logical - whether to report progress |
Gets read counts per sample from the "summary.txt" files output by featureCounts. This means you're getting counts for the features included in the annotation file given to featureCounts. This is how to get specifically intronic read counts, by giving featureCounts a gtf with only introns and then giving this function the resulting summary files. TIME:
Data frame - Columns correspond to input files and rows to read types
Emma Myers
1 2 3 4 5 6 | summaryFiles = list.files("NucSeq/counts/exonic_counts", pattern="summary")
fCounts = count_summaries(paste("NucSeq/counts/exonic_counts/", summaryFiles, sep=""))
assignedCounts = as.vector(fCounts[1,], mode="numeric")
pdf("NucSeq_assigned_reads_exonic.pdf")
barplot(assignedCounts/10^6, las=2, main="Nuc-seq exonic assigned reads", cex.names = 0.5, names.arg=gsub("_fcounts.txt.summary", "", summaryFiles), ylab="Millions")
dev.off()
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