atRegions {biscuiteer} | R Documentation |
Calls summarizeBsSeqOver to summarize a bsseq object over provided DNA regions. Useful for exploring genomic data using cBioPortal.
atRegions(bsseq, regions, mappings = NULL, nm = "POETICname", ...)
bsseq |
A bsseq object |
regions |
A GRanges or GRangesList of regions |
mappings |
A mapping table with rownames(mappings) == colnames(bsseq) (DEFAULT: NULL) |
nm |
Column of the mapping table to map to (DEFAULT: "POETICname") |
... |
Other arguments to pass to summarizeBsSeqOver |
GRanges with summarized information about the bsseq object for the given DNA regions
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) 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)) ) regions <- atRegions(bsseq = bisc, regions = reg)