convertLoc {iGenomicViewer} | R Documentation |
This function will convert genomic locations with respect to chromosome to genomic locations with respect to the entire genome or vice versa.
convertCloc(x, chr, row=TRUE, bandobj=NA) convertGloc(x, chr, row=TRUE, bandobj=NA)
x |
numeric vector or matrix of values |
chr |
indication of chromosome |
row |
when x is a matrix, should the chr value be applied by row or by column |
bandobj |
an object of the class bandinfo. if NA, useds iGenomicViewer's default band.info object |
Some applications require genomic locations to be with respect to the genome instead of by chromosome and vice versa. These functions provide a way to convert a numeric vector or matrix of one type to the other.
chr indicates which chromosome the value is on. If x is a vector, chr should be a vector of equal length, or a single value indicating all values of x are on the same chromosome. If x is a matrix, the values may be applied by row or by column. If by row, chr should be equal to dim(x)[1] and if by column, chr should be equal to dim(x)[2]. A single value may be used if all values are on the same chromosome.
The offset is calculated through the band.info object. See band.info for more information. If a bandobj is not specified the package's default bandinfo object is used.
vector or matrix, of same form as input, of converted values
Lori A. Shepherd
# # this is a mock example # x = matrix(0,24,3) x[,2] = 1 x[,3] = 2 # this is x before x chr = 1:24 newx = convertGloc(x=x, chr=chr, row=TRUE, bandobj=NA) # this is x after newx