Recode genotype information
function recode recodes bi-allelic genetic marker information
expressed as strings (e.g. "AA", "AB", "BB") into numerical form.
recode(X, alleles, values = c(0, 1, 2), pos1 = 1, pos2 = 3, minor = FALSE, verbose = FALSE)
X |
A matrix or dataframe of bi-allelic markers, individuals in rows, markers in columns |
alleles |
a vector with the alleles for each marker (e.g. c("A/T", "A/G", etc)) |
values |
a vector of numerica values for AA, AB and BB, ((0,1,2) by default). |
pos1 |
position of the first allele in the allele string (1 by default). |
pos2 |
position of the second allele in the allele string (3 by default). |
minor |
coding is according to the number of copies of the minor
allele. if |
verbose |
print progress on the conversion or not. |
recode is written for bi-allelic marker data
only. Heterozygotes may be coded both as AB or BA. By default, the
second allele specified (e.g. "T" in "A/T") is counted in the
recoding, and homozygotes AA are coded as 0 and homozygotes TT as 2.
A numerical matrix, individuals in rows, markers in columns
Jan Graffelman jan.graffelman@upc.edu
SNP1 <- c("GG","GG","GG","GG","GG","GG","GG","GG","GG")
SNP2 <- c("CG","GG","CC","GG","GG","CG","CG","CG","CG")
SNP3 <- c("AA","AA","AA","AG","AA","AG","AA","AA","AA")
SNP4 <- c("GG","GG","GG","GG","GG","GG","GG","GG","GG")
SNP5 <- c("CC","CC","CC","CC","CC","CC","CT","CT","CT")
X <- cbind(SNP1,SNP2,SNP3,SNP4,SNP5)
Y <- recode(X,c("A/G","C/G","A/G","A/G","C/T"))
print(Y)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.