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oligo (version 1.36.1)

chromosome2integer: Converts chromosome to integer

Description

Coerces character string for chromosome in the pd. annotation packages to integers

Usage

chromosome2integer(chrom)
        integer2chromosome(intChrom)

Arguments

chrom
A one or 2 letter character string (e.g, "1", "X", "Y", "MT", "XY")
intChrom
An integer vector with values 1-25 possible

Value

  • integer2chromosome returns a vector of character string indicating the chromosome the same length as intChrom. chromosome2integer returns a vector of integers the same length as the number of elements in the chrom vector.

Details

This is useful when sorting SNPs in an object by chromosome and physical position -- ensures that the sorting is done in the same way for different objects.

Examples

Run this code
chromosome2integer(c(1:22, "X", "Y", "XY", "M"))
	integer2chromosome(chromosome2integer(c(1:22, "X", "Y", "XY", "M")))

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