decodeCallCodes {GeneticsBase} | R Documentation |
Converts integer codes in a callCodes matrix to character string representations of geneSet.
decodeCallCodes(callCodes, transTables, markerInfo)
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". |
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.
Scott D. Chasalow
geneSet
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)