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Fix bugs in missingnessHeatMaps.R #9

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Fix bugs in missingnessHeatMaps.R #9

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16 changes: 12 additions & 4 deletions resources/missingnessHeatMaps.R
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ if (length(vcfFiles) > 1) {
matrixForBinding <- makeMatrix(vcfFiles[i], printStats = 0)

# Make sure that the full and intermediate matrices line up
if (!all.equal(colnames(matrixForBinding), colnames(superMatrix))) {
if (!identical(colnames(matrixForBinding), colnames(superMatrix))) {
stop("Col names don't match for ", args[1], " and ", args[i], ": Exiting now", call.=TRUE)
}

Expand Down Expand Up @@ -137,15 +137,23 @@ for (i in 1:length(vcfFiles)) {
snpgdsVCF2GDS(vcfFiles[i], gdsOut)

gdsInter <- snpgdsOpen(gdsOut)
# Compute the dendrogram:
ibsInter <- snpgdsHCluster(snpgdsIBS(gdsInter, num.thread=2))

# Compute IBS matrix
ibsInter.matOnly <- snpgdsIBS(gdsInter, num.thread=2, autosome.only=FALSE)

# If some values in IBS matrix are NA, change them to average IBS
ibs.ave <- mean(ibsInter.matOnly$ibs, na.rm=TRUE)
ibsInter.matOnly$ibs[is.na(ibsInter.matOnly$ibs)] <- ibs.ave

# Compute the dendrogram
ibsInter <- snpgdsHCluster(ibsInter.matOnly)

# Make the matrix
missingMatrix <- makeMatrix(vcfFiles[i], printStats = 0)
heatmapFile = paste(gsub(".vcf","", vcfFiles[i], fixed=T), '.heatmap', sep="")

# Print out the correlation coefficient of missingness as a function of relatedness:
missGenCorrelation <- cor(c(missingMatrix[lower.tri(missingMatrix, diag=F)]), c(ibsInter$dist[lower.tri(ibsInter$dist, diag = F)]), method="pearson")
missGenCorrelation <- cor(c(missingMatrix[lower.tri(missingMatrix, diag=F)]), c(ibsInter$dist[lower.tri(ibsInter$dist, diag = F)]), method="pearson", use="pairwise.complete.obs")
cat("Correlation (PCC) between missingness and genetic similarity for ", vcfFiles[i], ": ", missGenCorrelation, "\n", sep="")

# Plot the heatmaps
Expand Down