fixedWidthBins {chromstaR} | R Documentation

## Make fixed-width bins

### Description

Make fixed-width bins based on given bin size.

### Usage

    fixedWidthBins(bamfile = NULL, assembly = NULL, chrom.lengths = NULL,
      chromosome.format, binsizes = 1e+06, chromosomes = NULL)

### Arguments

`bamfile` | A BAM file from which the header is read to determine the chromosome lengths. If a `bamfile` is specified, option `assembly` is ignored.
`assembly` | An assembly from which the chromosome lengths are determined. Please see `fetchExtendedChromInfoFromUCSC` for available assemblies. This option is ignored if `bamfile` is specified. Alternatively a data.frame generated by `fetchExtendedChromInfoFromUCSC`.
`chrom.lengths` | A named character vector with chromosome lengths. Names correspond to chromosomes.
`chromosome.format` | A character specifying the format of the chromosomes if `assembly` is specified. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...). If a `bamfile` or `chrom.lengths` is supplied, the format will be chosen automatically.
`binsizes` | A vector of bin sizes in base pairs.
`chromosomes` | A subset of chromosomes for which the bins are generated.

### Value

A `list()` of `GRanges-class` objects with fixed-width bins.

### Author(s)

Aaron Taudt

### Examples

    ## Make fixed-width bins of size 500kb and 1Mb
    data(rn4_chrominfo)
    chrom.lengths <- rn4_chrominfo$length
    names(chrom.lengths) <- rn4_chrominfo$chromosome
    bins <- fixedWidthBins(chrom.lengths=chrom.lengths, binsizes=c(5e5,1e6))
    bins

    ## Make bins using NCBI server (requires internet connection)
    # bins <- fixedWidthBins(assembly='mm10', chromosome.format='NCBI', binsizes=c(5e5,1e6))

[Package chromstaR version 1.10.0 Index]