readBiscuit {biscuiteer} | R Documentation

## Read biscuit output into bsseq object

### Description

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).

### Usage

    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)

### 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)
`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)

### Details

NOTE: Assumes alignment against hg19 (use genome argument to override). NOTE: Requires header from VCF file to detect sample names

### Value

            A bsseq::BSseq object

### Functions

- `loadBiscuit`: Alias for readBiscuit

### See Also

bsseq

checkBiscuitBED

### 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")
      bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf,
                          merged = FALSE)

[Package biscuiteer version 1.1.0 Index]