show.ld.RdCalculate D' and R^2 for a SnpMatrix object and display as a heatmap
show.ld(X, snps = colnames(X), samples = rownames(X), lines.limit = 20)
| X | a SnpMatrix object |
|---|---|
| snps | optional character vector of column names of X (SNPs) for which LD should be calculated |
| samples | optional character vector of row names of X (Samples) for which LD should be calculated |
| lines.limit | draw faint lines to make separation between SNPs clearer if the number of SNPs is < lines.limit |
invisibly returns matrix with D' in upper.tri() entries and R^2 in lower.tri() entries
Side effect: displays plot on current graphics device