makeBSseq {biscuiteer} | R Documentation |
Beware that any reasonably large BED files may not fit into memory!
makeBSseq(tbl, params, simplify = FALSE, verbose = FALSE)
tbl |
A tibble (from read_tsv) or a data.table (from fread) |
params |
Parameters from checkBiscuitBED |
simplify |
Simplify sample names by dropping .foo.bar.hg19? (or similar) (DEFAULT: FALSE) |
verbose |
Print extra statements? (DEFAULT: FALSE) |
An in-memory bsseq object
library(data.table) library(R.utils) 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") params <- checkBiscuitBED(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE, how = "data.table") select <- grep("\\.context", params$colNames, invert=TRUE) tbl <- fread(gunzip(params$tbx$path, remove = FALSE), sep="\t", sep2=",", fill=TRUE, na.strings=".", select=select) unzippedName <- sub("\\.gz$", "", params$tbx$path) if (file.exists(unzippedName)) { file.remove(unzippedName) } if (params$hasHeader == FALSE) names(tbl) <- params$colNames[select] names(tbl) <- sub("^#", "", names(tbl)) tbl <- tbl[rowSums(is.na(tbl)) == 0, ] bsseq <- makeBSseq(tbl = tbl, params = params)