Add set operation for MAFs

DESCRIPTION

@@ -22,7 +22,7 @@ Imports:
     wordcloud,
     grDevices,
     survival
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+RoxygenNote: 7.1.0
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R/setMaf.R

@@ -0,0 +1,114 @@
+#' Set Operations for MAF objects
+#' @param x the first `MAF` object.
+#' @param y the second `MAF` object.
+#' @param ... other parameters passing to `subsetMaf` for subsetting operations.
+#' @name setMaf
+#' @examples
+#' laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
+#' laml <- read.maf(maf = laml.maf)
+#' x <- subsetMaf(maf = laml, tsb = c('TCGA-AB-3009'))
+#' y <- subsetMaf(maf = laml, tsb = c('TCGA-AB-2933'))
+#' setdiffMAF(x, y)
+#' intersectMAF(x, y)
+#' # This is similar to merge_mafs()
+#' unionMAF(x, y)
+NULL
+
+
+#' @rdname setMaf
+setdiffMAF <- function(x, y, mafObj = TRUE, ...) {
+ stopifnot(inherits(x, "MAF"), inherits(y, "MAF"))
+
+  args = list(...)
+  if (length(args) == 0) {
+    maf_x = rbind(x@data, x@maf.silent)
+    maf_y = rbind(y@data, y@maf.silent)
+  } else {
+    maf_x = subsetMaf(x, mafObj = FALSE, ...)
+    maf_y = subsetMaf(y, mafObj = FALSE, ...)
+  }
+
+  maf_x[, Label := paste(Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2, Variant_Type)]
+  maf_y[, Label := paste(Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2, Variant_Type)]
+
+  set = setdiff(maf_x$Label, maf_y$Label)
+
+  if (length(set) == 0) {
+    message("No variants left.")
+    return(NULL)
+  }
+
+  maf_x = maf_x[Label %in% set]
+  maf_x$Label = NULL
+
+  if (!mafObj) {
+    maf_x
+  } else {
+    return(read.maf(maf_x, clinicalData = x@clinical.data, verbose = FALSE))
+  }
+}
+
+#' @rdname setMaf
+unionMAF <- function(x, y, mafObj = TRUE, ...) {
+  stopifnot(inherits(x, "MAF"), inherits(y, "MAF"))
+
+  args = list(...)
+
+  if (length(args) == 0) {
+    maf_x = rbind(x@data, x@maf.silent)
+    maf_y = rbind(y@data, y@maf.silent)
+  } else {
+    maf_x = subsetMaf(x, mafObj = FALSE, ...)
+    maf_y = subsetMaf(y, mafObj = FALSE, ...)
+  }
+
+  maf = unique(rbind(maf_x, maf_y, fill = TRUE))
+
+  if (!mafObj) {
+    return(maf)
+  } else {
+    cli_merged = rbind(x@clinical.data, y@clinical.data)
+    return(read.maf(maf, clinicalData = cli_merged, verbose = FALSE))
+  }
+
+}
+
+
+#' @rdname setMaf
+#'
+intersectMAF <- function(x, y, mafObj = TRUE, ...) {
+  stopifnot(inherits(x, "MAF"), inherits(y, "MAF"))
+
+  args = list(...)
+  if (length(args) == 0) {
+    maf_x = rbind(x@data, x@maf.silent)
+    maf_y = rbind(y@data, y@maf.silent)
+  } else {
+    maf_x = subsetMaf(x, mafObj = FALSE, ...)
+    maf_y = subsetMaf(y, mafObj = FALSE, ...)
+  }
+
+  maf_x[, Label := paste(Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2, Variant_Type)]
+  maf_y[, Label := paste(Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2, Variant_Type)]
+
+  set = intersect(maf_x$Label, maf_y$Label)
+  if (length(set) == 0) {
+    message("No common variants found.")
+    return(NULL)
+  }
+
+  maf_x = maf_x[Label %in% set]
+  maf_x$Label = NULL
+  maf_y = maf_y[Label %in% set]
+  maf_y$Label = NULL
+
+
+  maf = rbind(maf_x, maf_y, fill = TRUE)
+  if (!mafObj) {
+    return(maf)
+  } else {
+    cli_merged = rbind(x@clinical.data, y@clinical.data)
+    return(read.maf(maf, clinicalData = cli_merged, verbose = FALSE))
+  }
+
+}