fixedWidthBins: Make fixed-width bins

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

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 getChromInfoFromUCSC for available assemblies. This option is ignored if bamfile is specified. Alternatively a data.frame generated by getChromInfoFromUCSC.
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))

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.