humarray (version 1.0.0)

force.chr.pos: Force a valid genomic range, given the inputted coordinates

Description

Enter a pair of genomic locations representing a range for a given chromosome and this function will ensure that no position is less than 1 or greater than the relevant chromosome lengths. Anything below will be coerced to 1, and anything above to the chromosome length.

Usage

force.chr.pos(Pos, Chr, snp.info = NULL, build = NULL, dir = NULL)

Arguments

Pos

must be numeric, length 2, e.g, c(20321,30123)

Chr

chromosome label

snp.info

optional object to take boundaries from, the maxima and minima for each chromosome within this object will take the place of the chromsome lengths / 1.

build

ucsc build, only need to enter if this differs from getOption("ucsc")

dir

directory to use for download of chromosome lengths (only if you wish to keep the chromosome length file)

Examples

pss <- ps <- c(345035,345035); ch <- 1
force.chr.pos(ps,ch)
pss[1] <- 0
force.chr.pos(pss,ch) # won't allow zero
pss[1] <- -1
force.chr.pos(pss,ch) # won't allow negative
pss[1] <- 645035012
force.chr.pos(pss,ch) # won't allow pos > chromosome length