fixedWidthBins {chromstaR} | R Documentation |
Make fixed-width bins based on given bin size.
fixedWidthBins(bamfile = NULL, assembly = NULL, chrom.lengths = NULL, chromosome.format, binsizes = 1e+06, chromosomes = NULL)
bamfile |
A BAM file from which the header is read to determine the chromosome lengths. If a |
assembly |
An assembly from which the chromosome lengths are determined. Please see |
chrom.lengths |
A named character vector with chromosome lengths. Names correspond to chromosomes. |
chromosome.format |
A character specifying the format of the chromosomes if |
binsizes |
A vector of bin sizes in base pairs. |
chromosomes |
A subset of chromosomes for which the bins are generated. |
A list()
of GRanges-class
objects with fixed-width bins.
Aaron Taudt
## 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))