diff --git a/DESCRIPTION b/DESCRIPTION
index f545c09..50d00a5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,7 +22,7 @@ Imports:
     wordcloud,
     grDevices,
     survival
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Encoding: UTF-8
 Suggests: knitr, rmarkdown, BSgenome, Biostrings, NMF, mclust, berryFunctions
 VignetteBuilder: knitr
diff --git a/R/setMaf.R b/R/setMaf.R
new file mode 100644
index 0000000..64c6b2d
--- /dev/null
+++ b/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))
+  }
+
+}
diff --git a/man/setMaf.Rd b/man/setMaf.Rd
new file mode 100644
index 0000000..071581e
--- /dev/null
+++ b/man/setMaf.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setMaf.R
+\name{setMaf}
+\alias{setMaf}
+\alias{setdiffMAF}
+\alias{unionMAF}
+\alias{intersectMAF}
+\title{Set Operations for MAF objects}
+\usage{
+setdiffMAF(x, y, mafObj = TRUE, ...)
+
+unionMAF(x, y, mafObj = TRUE, ...)
+
+intersectMAF(x, y, mafObj = TRUE, ...)
+}
+\arguments{
+\item{x}{the first `MAF` object.}
+
+\item{y}{the second `MAF` object.}
+
+\item{...}{other parameters passing to `subsetMaf` for subsetting operations.}
+}
+\description{
+Set Operations for MAF objects
+}
+\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)
+}