readBiscuit {biscuiteer} | R Documentation |
Takes BED-like format with 2 or 3 columns per sample. Unmerged CpG files have 2 columns (beta values and coverage), whereas merged CpG files have 3 columns (beta values, coverage, and context).
readBiscuit( BEDfile, VCFfile, merged, sampleNames = NULL, simplify = FALSE, genome = "hg19", how = c("data.table", "readr"), hdf5 = FALSE, hdf5dir = NULL, sparse = FALSE, chunkSize = 1e+06, chr = NULL, which = NULL, verbose = FALSE ) loadBiscuit( BEDfile, VCFfile, merged, sampleNames = NULL, simplify = FALSE, genome = "hg19", how = c("data.table", "readr"), hdf5 = FALSE, hdf5dir = NULL, sparse = FALSE, chunkSize = 1e+06, chr = NULL, which = NULL, verbose = FALSE )
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) |
simplify |
Simplify sample names by dropping .foo.bar.hg19? (or similar) (DEFAULT: FALSE) |
genome |
Genome assembly the runs were aligned against (DEFAULT: "hg19") |
how |
How to load data - either data.table or readr (DEFAULT: "data.table") |
hdf5 |
Make the object HDF5-backed - CURRENTLY NOT AVAILABLE (DEFAULT: FALSE) |
hdf5dir |
Directory to store HDF5 files if 'hdf5' = TRUE (DEFAULT: NULL) |
sparse |
Use sparse Matrix objects for the data? (DEFAULT: FALSE) |
chunkSize |
Number of rows before readr reading becomes chunked (DEFAULT: 1e6) |
chr |
Load a specific chromosome? (DEFAULT: NULL) |
which |
A GRanges of regions to load - NULL loads them all (DEFAULT: NULL) |
verbose |
Print extra statements? (DEFAULT: FALSE) |
NOTE: Assumes alignment against hg19 (use genome argument to override). NOTE: Requires header from VCF file to detect sample names
A bsseq::BSseq object
loadBiscuit
: Alias for readBiscuit
bsseq
checkBiscuitBED
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") bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE)