Description Usage Arguments Value Examples
Calls summarizeBsSeqOver to summarize a bsseq object over provided DNA regions. Useful for exploring genomic data using cBioPortal.
1 |
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 |
1 2 |
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
|
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