#' @include mpcross-class.R
print.mpcrossLG <- function(x)
{
cat("This mpcross object contains linkage groups\n")
callNextMethod()
}
setMethod(f = "print", signature = "mpcrossLG", definition = print.mpcrossLG)
print.mpcrossRF <- function(x)
{
cat("This mpcross object contains recombination fractions\n\n")
callNextMethod()
}
setMethod(f = "print", signature = "mpcrossRF", definition = print.mpcrossRF)
print.mpcross <- function(x)
{
nGeneticDatasets <- length(x@geneticData)
nLines <- nLines(x)
if(nGeneticDatasets == 1)
{
missingInFounders <- apply(x@geneticData[[1]]@founders, 2, function(y) any(is.na(y)))
founderAlleles <- apply(x@geneticData[[1]]@founders, 2, function(y) length(unique(y)))
proportionMissing <- apply(x@geneticData[[1]]@finals, 2, function(y) sum(is.na(y)) / nLines)
cat("-------------------------------------------------------\n")
cat("Summary of mpcross object\n")
cat("-------------------------------------------------------\n")
cat(sum(missingInFounders), " markers had missing values in founders\n")
cat(sum(founderAlleles==1), " markers had non-polymorphic founder genotypes\n")
cat("-------------------------------------------------------\n")
cat(sum(founderAlleles==2), " markers were biallelic.\n")
cat(sum(founderAlleles > 2), " markers were multiallelic.\n")
cat("-------------------------------------------------------\n")
cat(sum(proportionMissing>.05), " markers had >5% missing data.\n")
cat(sum(proportionMissing>.10), " markers had >10% missing data.\n")
cat(sum(proportionMissing>.20), " markers had >20% missing data.\n")
} else
{
cat("This mpcross object contains", nGeneticDatasets, " genetic data sets\n")
for(i in 1:nGeneticDatasets)
{
missingInFounders <- apply(x@geneticData[[i]]@founders, 2, function(y) any(is.na(y)))
founderAlleles <- apply(x@geneticData[[i]]@founders, 2, function(y) length(unique(y)))
proportionMissing <- apply(x@geneticData[[i]]@finals, 2, function(y) sum(is.na(y)) / nLines[i])
cat("\n-------------------------------------------------------\n")
cat("Summary of data set", i, "\n")
cat("-------------------------------------------------------\n")
cat(sum(missingInFounders), " markers had missing values in founders\n")
cat(sum(founderAlleles==1), " markers had non-polymorphic founder genotypes\n")
cat("-------------------------------------------------------\n")
cat(sum(founderAlleles==2), " markers were biallelic.\n")
cat(sum(founderAlleles > 2), " markers were multiallelic.\n")
cat("-------------------------------------------------------\n")
cat(sum(proportionMissing>.05), " markers had >5% missing data.\n")
cat(sum(proportionMissing>.10), " markers had >10% missing data.\n")
cat(sum(proportionMissing>.20), " markers had >20% missing data.\n")
}
}
}
setMethod(f = "print", signature = "mpcross", definition = print.mpcross)
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