count_coverage {ChromSCape} | R Documentation |
Normalization is CPM, smoothing is done by averaging on n_smoothBin regions left and right of any given region.
count_coverage( filename, format = "BAM", bins, canonical_chr, n_smoothBin = 5, ref = "hg38", read_size = 101 )
filename |
Path towards the BAM to create coverage from |
format |
File format, either "BAM" or "BED" |
bins |
A GenomicRanges object of binned genome |
canonical_chr |
GenomicRanges of the chromosomes to read the BAM file. |
n_smoothBin |
Number of bins left and right to smooth the signal. |
ref |
Genomic reference |
read_size |
Length of the reads |
A binned GenomicRanges that can be readily exported into bigwig file.