rres (version 1.1)

recode.snpdata: Recode SNP marker data.

Description

recode.snpdata recodes SNP marker data for use with other functions in this package.

Usage

recode.snpdata(data, snp.major = FALSE, ma.ref = FALSE,
  input.haplotype = FALSE, output.allele = TRUE, output.haplotype = FALSE,
  na.string = NULL)

Arguments

data

numeric matrix or dataframe.

snp.major

logical.

ma.ref

logical.

input.haplotype

logical.

output.allele

logical.

output.haplotype

logical.

na.string

numeric or character vector.

Value

A list of two elements. First element named data is a matrix of recoded marker data in specified format. Second element is a dataframe named alleles that specifies reference/alternate alleles at all markers.

Details

The standard marker data used by other functions of this package takes one of three forms: (a) subjects by row, counts of reference alleles by column; (b) subjects by row, allelic types (2 per marker) by column; (c) haplotypes (2 per subject) by row, allelic types by column. Reference alleles are coded 1, alternate alleles are coded 2.

By default, snp.major = FALSE, set it to TRUE if input matrix has SNPs by row and allelic types (2 per subject) by column. ma.ref = FALSE, set it to TRUE if the minor allele is to be the reference allele. input.haplotype = FALSE, set it to TRUE if input matrix has haplotypes (2 per subject) by row and allelic types by column. output.allele = TRUE, set it to FALSE if counts of reference alleles is the desired output format. output.haplotype = FALSE, set it to TRUE if recoded marker data by haplotype is the desired output format. input.haplotype is only invoked when snp.major = FALSE. output.haplotype is only invoked when output.allele = TRUE.

Examples

# NOT RUN {
test.dat = matrix(c(3,4,4,3), 4, 10)

# treat test.dat as 4 input haplotypes of two subjects at 10 SNP markers,
# output recoded data as haplotypes
recode.snpdata(test.dat, input.haplotype = TRUE, output.haplotype = TRUE)

# treat test.dat as 4 input haplotypes of two subjects at 10 SNP markers,
# output recoded data as counts of reference alleles
recode.snpdata(test.dat, input.haplotype = TRUE, output.allele = FALSE)
#'
# treat test.dat as allelic types at 5 SNPs of 4 subjects,
# output recoded data as haplotypes
recode.snpdata(test.dat, output.haplotype = TRUE)
# }