read.biscuit: a bsseq loader for Biscuit output (BED-like format, 2 or 3...
In ttriche/biscuitEater: a bunch of convenience functions for Biscuit

Description Usage Arguments Value See Also

e.g. P01-028-T06.joint.ch.hg19.bed.gz has 3 samples, and 9 columns total, while P01-028-T06.joint.cg.merged.hg19.bed.gz has 3 samples and 12 columns. Note: the defaults assume alignment against hg19 (use genome=xyz to override) Note 2: if a BED has no header, a VCF header can be used to autodetect names.

read.biscuit(BEDfile, VCFfile = NULL, sampleNames = NULL,
  simplify = FALSE, genome = "hg19", how = c("data.table", "readr"),
  hdf5 = FALSE, hdf5dir = NULL, sparse = FALSE, merged = NULL,
  chunkSize = 1e+06, chr = NULL, which = NULL, verbose = FALSE)

`BEDfile`	the file (compressed or not, doesn't matter) to load
`VCFfile`	the file (compressed and tabixed, with header) to load
`sampleNames`	if NULL, create; if VCF, read; if data.frame, make pData
`simplify`	simplify sample names by dropping .foo.bar.hg19 or similar
`genome`	what genome assembly were the runs aligned against? (hg19)
`how`	how to load the data? "data.table" (default) or "readr"
`hdf5`	make the object HDF5-backed? (FALSE; use in-core storage)
`hdf5dir`	if hdf5 is TRUE, where should HDF5 files be stored? (NULL)
`sparse`	are there a lot of zero-coverage sites? (default is FALSE)
`merged`	are CpG sites merged? (default NULL; figure out from BED)
`chunkSize`	number of rows before readr reading becomes chunked (1e6)
`chr`	load a specific chromosome (to rbind() later)? (NULL)
`which`	a GRanges of regions to load (default NULL, load them all)
`verbose`	be verbose? (FALSE)