coverage(reads, annotation, sf = NULL, outfile = NULL)
Arguments
reads
a data.table of values
or a character vector indicating the input file name.
Note: the data must be in a BED-like format.
annotation
a object of type annotationsSet
or a character vector indicating the input BED file name.
sf
a number indicating the scaling factor.
Each coverage value is multiplied by this factor before being reported.
Useful for normalizing coverage by, e.g., reads per million (RPM).
outfile
a character vector indicating the output file name.
If not provided, the result will be internalized in R.
Value
An object of type data.table with 8 columns,
corresponding to: