decodeCallCodes {GeneticsBase}R Documentation

Converts integer codes in a callCodes matrix to character string representations of geneSet.

Description

Converts integer codes in a callCodes matrix to character string representations of geneSet.

Usage

decodeCallCodes(callCodes, transTables, markerInfo)

Arguments

callCodes matrix of positive integers, such as the callCodes slot of a geneSet object.
transTables list of code translation tables, such as the transTables slot of a geneSet object.
markerInfo dataframe, with one row for each row in the callCodes matrix, such as the markerInfo slot of a geneSet object. Must include at least column "TransTable".

Value

a character matrix with the same dimension and dimnames as argument callCodes, giving character string representations of genotypes, as specified by a set of translation tables.

Author(s)

Scott D. Chasalow

See Also

geneSet

Examples

library(GeneticsBase)
tTabList <- makeTransTableList(c("Bb", "ATG"), c("Generic", "SNP"))
locus <- c("c104t", "c2249t")
ttab <- c("SNP", "Generic")
minfo <- makeMarkerInfo(locus, ttab)
misscodes <- list(Generic = c("NA", ".", "-"), SNP = "N")
r1 <- c(1, 2, 1, 1)
r2 <- c(1, 2, 3, 2)
data <- rbind(r1, r2) # callCodes
dimnames(data) <- list(locus, paste("Sample", seq(along = r1),
        sep = "."))
decodeCallCodes(data, tTabList, minfo)

[Package GeneticsBase version 1.8.0 Index]