HOMER can produce tag counts of selected regions (tss or from peak files). ReadCounts will read this data in tidy up the column names and cast the matrix as numeric, and finally return a data.table object for use with other functions.

ReadCounts(counts.raw)

Arguments

counts.raw

Location of raw tag counts data from HOMER.

Value

data.table of counts data with annotation and tidy columns.

Details

This counts table can be produced using the homer_quant.sh script from the NewSeq pipeline, which runs the following command over multiple tag directories: annotatePeaks.pl tss mm10 -ann $GTF -size $SIZE -log -d $TAGDIRS