makeBSseq {biscuiteer} | R Documentation

## Make an in-memory bsseq object from a biscuit BED

### Description

Beware that any reasonably large BED files may not fit into memory!

### Usage

    makeBSseq(tbl, params, simplify = FALSE, verbose = FALSE)

### Arguments

`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)

### Value

         An in-memory bsseq object

### Examples

      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)

[Package biscuiteer version 1.2.0 Index]