checkBiscuitBED: Inspect Biscuit VCF and BED files
In biscuiteer: Convenience Functions for Biscuit

Description Usage Arguments Details Value See Also Examples

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.

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

`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)

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

1	Parameters to be supplied to makeBSseq

readBiscuit

  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)