checkBiscuitBED {biscuiteer} | R Documentation

## Inspect Biscuit VCF and BED files

### Description

A BED checker for Biscuit CpG/CpH output (BED-like format with 2 or 3 columns per sample). By default, files with more than 50 million loci will be processed iteratively, since data.table tends to run into problems with gzipped joint CpH files.

### Usage

    checkBiscuitBED(
      BEDfile,
      VCFfile,
      merged,
      sampleNames = NULL,
      chunkSize = 5e+07,
      hdf5 = FALSE,
      sparse = TRUE,
      how = c("data.table", "readr"),
      chr = NULL
    )

### Arguments

`BEDfile` | A BED-like file - must be compressed and tabix'ed
`VCFfile` | A VCF file - must be compressed and tabix'ed. Only the header information is needed.
`merged` | Is this merged CpG data?
`sampleNames` | Names of samples - NULL: create names, vector: assign names, data.frame: make pData (DEFAULT: NULL)
`chunkSize` | For files longer than `yieldSize` number of lines long, chunk the file (DEFAULT: 5e7)
`hdf5` | Use HDF5 arrays for backing the data? Using HDF5-backed arrays stores the data in a HDF5 file on disk, rather than loading entire object into memory. This allows for analyses to be done on memory-limited systems at the small cost of slightly reduced return times. (DEFAULT: FALSE)
`sparse` | Use sparse Matrix objects for the data? If TRUE, use a Matrix object for sparse matrices (matrices with many zeroes in them) (DEFAULT: TRUE)
`how` | How to load the data - "data.table" or "readr"? (DEFAULT: data.table)
`chr` | Load a specific chromosome to rbind() later? (DEFAULT: NULL)

### Details

Input BED and VCF files must be tabix'ed. No exceptions!

### Value

            Parameters to be supplied to makeBSseq

### See Also

readBiscuit

### Examples

      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)

[Package biscuiteer version 1.4.0 Index]