Make fixed-width bins

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Description

Make fixed-width bins based on given bin size.

Usage

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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 objects with fixed-width bins.

Author(s)

Aaron Taudt

Examples

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## Make fixed-width bins of size 500kb and 1Mb
bins <- fixedWidthBins(assembly='mm10', chromosome.format='NCBI', binsizes=c(5e5,1e6))
bins

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