binCoverage {biscuiteer} | R Documentation |
Example usage for E-M
binCoverage( bsseq, bins, which = NULL, QDNAseq = TRUE, readLen = 100, paired = TRUE )
bsseq |
A bsseq object - supplied to getCoverage() |
bins |
Bins to summarize over - from tileGenome or QDNAseq.xxYY |
which |
Limit to specific regions? - functions as an import() (DEFAULT: NULL) |
QDNAseq |
Return a QDNAseqReadCounts? - if FALSE, returns a GRanges (DEFAULT: TRUE) |
readLen |
Correction factor for coverage - read length in bp (DEFAULT: 100) |
paired |
Whether the data are from paired-end sequencing (DEFAULT: TRUE) |
NOTE: As of early Sept 2019, QDNAseq did not have hg38 capabilities. If you desire to use the hg38 genome, biscuiteer suggests you use a GRanges object to define your bins.
NOTE: As of late July 2020, biscuiteer has started implemented support for hg38, hg19, mm10, and mm9 for bisulfite-specific features, including adaptive GC-content computation and SV integration for adjusting CNV ends.
Binned read counts
bins <- GRanges(seqnames = rep("chr11",10), strand = rep("*",10), ranges = IRanges(start=100000*0:9, width=100000) ) reg <- GRanges(seqnames = rep("chr11",5), strand = rep("*",5), ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7), end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7)) ) orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz", package="biscuiteer") orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz", package="biscuiteer") bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE) bc <- binCoverage(bsseq = bisc, bins = bins, which = reg, QDNAseq = FALSE)