humarray (version 1.2)

chrNums: Extract chromosome numbers from GRanges/RangedData

Description

Sometimes chromosomes are codeds as 1:22, sometimes there is also X,Y, etc, sometimes it's chr1, ch2, etc. This function extracts the set of chromosome labels used by a ranged object (ie, GRanges or RangedData) and converts the labels to numbers in a consistent way, so 1:22, X, Y, XT, MT ==> 1:26, and optionally you can output the conversion table of codes to numbers, then input this table for future conversions to ensure consistency.

Usage

chrNums(ranged, warn = FALSE, table.out = FALSE, table.in = NULL)

Arguments

ranged

GRanges or RangedData object

warn

logical, whether to display a warning when non autosomes are converted to numbers

table.out

logical, whether to return a lookup table of how names matched to integers

table.in

data.frame/matrix, col 1 is the raw text names, col 2 is the integer that should be assigned, col 3 is the cleaned text (of col 1) with 'chr' removed. the required form is outputted by this function if you set 'table.out=TRUE', so the idea is that to standardize coding amongst several RangedData objects you can save the table each time and ensure future coding is consistent with this. Note that chromosomes 1-22, X, Y, XY, and MT are always allocated the same integer, so table is only useful where there are extra NT, COX, HLA regions, etc.

Value

a set of integers of length equal to the number of unique chromosomes in the ranged data.

Examples

# NOT RUN {
require(genoset)
gg <- rranges(1000)
chrNames(gg); chrNums(gg)
gg <- rranges(1000,chr.pref=TRUE) # example where chromosomes are chr1, chr2, ...
chrNames(gg); chrNums(gg)
lookup <- chrNums(gg,table.out=TRUE)
lookup
gg2 <- rranges(10)
chrNums(gg2,table.in=lookup) # make chromosome numbers using same table as above
# }