checkBiscuitBED: Inspect Biscuit VCF and BED files

In trichelab/biscuiteer: Convenience Functions for Biscuit

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)

trichelab/biscuiteer documentation built on March 4, 2024, 12:22 a.m.