recodeChromosome: Change chromosomal coding

In GenABEL: genome-wide SNP association analysis

Description

Recoding of chromosomes according to the provided 'rules' for from -> to pairs. Most common use is anticipated when importing data from other software using only integers to represent chromosomes. In this situation the list of rules may look like this: list(24="X",25="Y",26="mt").

Usage

  recodeChromosome(data, rules, quiet = FALSE)

Arguments

data	object of class for which 'chromosome' method is defined, e.g. 'gwaa.data', 'snp.data', 'scan.gwaa'
rules	list of pairs 'from=to'; the chromosomes coded in the original data set with 'from' will be recoded with 'to' value
quiet	if summary of recoding should not be printed to the screen

Value

modified 'data' object

Note

'from' entries should be unique and not overlap with entries in 'to'

Author(s)

Yurii Aulchenko

Examples

require(GenABEL.data)
data(ge03d2)
table(chromosome(ge03d2))
# merge chromosome 3 and X, call chromosome 2 as 15
newdat <- recodeChromosome(ge03d2,rules=list("3"="X","2"=15))
table(chromosome(ge03d2),chromosome(newdat))

GenABEL documentation built on May 30, 2017, 3:36 a.m.