humarray (version 1.2)

set.chr.to.numeric: Change the chromosome labels in a RangedData or GRanges object to numbers

Description

Change the chromosome labels in a RangedData or GRanges object to numbers

Usage

set.chr.to.numeric(ranged, keep = T, table.in = NULL, table.out = FALSE)

Arguments

ranged

A GRanges or RangedData object

keep

logical, whether to keep additional metadata columns in the new object

table.in

matrix/data.frame object, usually a result of a prior run of set.chr.to.numeric(table.out=TRUE), which shows for each label (column 1), what chromosome number should correspond. A way of ensuring consistent coding in different sets.

table.out

logical, if FALSE, the output will just be the object with updated chromosome labels. If TRUE, then the output will be a list, where the first element is the updated object and the second object is a table describing the coding scheme used to convert from labels to numeric indices.

Value

returns the 'ranged' object, but wherever a chromosome label was previously a character label, e.g, 'chr1', or 'X', will return as a number, e.g, 1 or 23 respectively. If table.out is TRUE will return a list where the first element is the resulting object, and the second element is a table showing which labels were converted to what number. This table can then be used for future conversions via the parameter 'table.in' to ensure consistency of coding.

See Also

set.chr.to.char

Examples

# NOT RUN {
char <- rranges(chr.pref=TRUE)
char
set.chr.to.numeric(char)
# behaviour with X, Y, etc
char <- rranges(chr.range=c(20:26))
#' char
set.chr.to.numeric(char)
tab <- set.chr.to.numeric(char,table.out=TRUE)[[2]]
tab # codes used in conversion #
char <- rranges(chr.range=c(20:26))
set.chr.to.numeric(char, table.in=tab) # code using codes from 'tab'
# }