[Genabel-commits] r1176 - pkg/GenABEL/R

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-04-02 18:10:59 +0200 (Tue, 02 Apr 2013)
New Revision: 1176

Modified:
   pkg/GenABEL/R/export.plink.R
Log:
GenABELs export.plink() function: brought code more in line with the
(proposed) coding standards. No functional changes, only code layout.
This is a preparation for my next commit.


Modified: pkg/GenABEL/R/export.plink.R
===================================================================
--- pkg/GenABEL/R/export.plink.R	2013-03-26 13:38:42 UTC (rev 1175)
+++ pkg/GenABEL/R/export.plink.R	2013-04-02 16:10:59 UTC (rev 1176)
@@ -1,69 +1,93 @@
 #' Export GenABEL data in PLINK format
-#' 
-#' Export GenABEL data in PLINK format. This function is 
-#' a simple wrapper to \code{\link{export.merlin}} function 
-#' with specific arguments + few lines of code to 
+#'
+#' Export GenABEL data in PLINK format. This function is
+#' a simple wrapper to \code{\link{export.merlin}} function
+#' with specific arguments + few lines of code to
 #' export phenotypes
-#' 
-#' @param data GenABEL data object of 'gwaa.data'-class to 
+#'
+#' @param data GenABEL data object of 'gwaa.data'-class to
 #' be exported
-#' 
-#' @param filebasename base file name for exported data, 
-#' extensions '.ped', '.map' and '.phe' (for phenotype file) 
+#'
+#' @param filebasename base file name for exported data,
+#' extensions '.ped', '.map' and '.phe' (for phenotype file)
 #' are added for specific output files
-#' 
-#' @param phenotypes NULL (no phenotypes exported), "all" for 
-#' all phenotypes or a vector of character with names of phneotypes 
-#' to be exported 
-#' 
-#' @param transpose if FALSE, regular 'tped' files produced, else 
-#' 'ped' files are produced 
-#' 
-#' @param export012na if true, export in numeric (0, 1, 2, NA) format 
+#'
+#' @param phenotypes NULL (no phenotypes exported), "all" for
+#' all phenotypes or a vector of character with names of phneotypes
+#' to be exported
+#'
+#' @param transpose if FALSE, regular 'tped' files produced, else
+#' 'ped' files are produced
+#'
+#' @param export012na if true, export in numeric (0, 1, 2, NA) format
 #' (as opposed to ATGC format)
-#' 
+#'
 #' @param ... arguments passed to \code{\link{export.merlin}}
-#' 
+#'
 #' @author Yurii Aulchenko
-#' 
+#'
 #' @keywords IO
-#' 
+#'
 
-"export.plink" <- function(data, filebasename="plink", phenotypes= "all", 
-		transpose=FALSE, export012na=FALSE, ...) 
+"export.plink" <- function(data, filebasename="plink", phenotypes= "all",
+                           transpose=FALSE, export012na=FALSE, ...)
 {
-	
-	if (!is.null(phenotypes)) {
-		phef <- paste(filebasename,".phe",sep="")
-		phed <- phdata(data)
-		phed <- data.frame(FID=seq(1:dim(phed)[1]),IID=phed[,"id"],
-				phed[,which(names(phed) != "id")])
-		if (phenotypes != "all") {
-			phed <- phed[,c("FID","IID",phenotypes)]
-		}
-		write.table(phed,file=phef,row.names=FALSE,col.names=TRUE,quote=FALSE,sep=" ")
-	}
-	
-	if (!transpose) {
-		pedf <- paste(filebasename,".ped",sep="")
-		mapf <- paste(filebasename,".map",sep="")
-		
-		export.merlin(data,pedfile=pedf,datafile=NULL,
-				mapfile=mapf,format="plink", ... )
-	} else {
-		# export TFAM
-		sx <- male(data)
-		sx[sx==0] <- 2
-		tfam <- data.frame(FID=c(1:nids(data)),IID=idnames(data),father=0,mother=0,
-				sex=sx,trait=-9,stringsAsFactors=FALSE)
-		write.table(tfam,file=paste(filebasename,".tfam",sep=""),row.names=FALSE,
-				col.names=FALSE,quote=FALSE)
-		# export genotypic data
-		pedfilename <- paste(filebasename,".tped",sep="")
-		tmp <- .Call("export_plink_tped",as.character(snpnames(data)), as.character(chromosome(data)), 
-				as.double(map(data)),as.raw(gtdata(data)@gtps), as.integer(nsnps(data)), 
-				as.integer(nids(data)), as.character(coding(data)), as.character(pedfilename), 
-				as.logical(export012na))
-	}
-	
-}
\ No newline at end of file
+
+  if (!is.null(phenotypes)) {
+    phef <- paste(filebasename, ".phe", sep="")
+    phed <- phdata(data)
+    phed <- data.frame(FID=seq(1:dim(phed)[1]),
+                       IID=phed[, "id"],
+                       phed[, which(names(phed) != "id")])
+
+    if (phenotypes != "all") {
+      phed <- phed[, c("FID", "IID", phenotypes)]
+    }
+
+    write.table(phed,
+                file=phef,
+                row.names=FALSE,
+                col.names=TRUE,
+                quote=FALSE,
+                sep=" ")
+  }
+
+  if (!transpose) {
+    pedf <- paste(filebasename, ".ped", sep="")
+    mapf <- paste(filebasename, ".map", sep="")
+
+    export.merlin(data,
+                  pedfile=pedf,
+                  datafile=NULL,
+                  mapfile=mapf,
+                  format="plink", ... )
+  } else {
+    ## export TFAM
+    sx <- male(data)
+    sx[sx==0] <- 2
+    tfam <- data.frame(FID=c(1:nids(data)),
+                       IID=idnames(data),
+                       father=0,
+                       mother=0,
+                       sex=sx,
+                       trait=-9,
+                       stringsAsFactors=FALSE)
+    write.table(tfam,
+                file=paste(filebasename, ".tfam", sep=""),
+                row.names=FALSE,
+                col.names=FALSE,
+                quote=FALSE)
+    ## export genotypic data (TPED)
+    pedfilename <- paste(filebasename, ".tped", sep="")
+    tmp <- .Call("export_plink_tped",
+                 as.character(snpnames(data)),
+                 as.character(chromosome(data)),
+                 as.double(map(data)),
+                 as.raw(gtdata(data)@gtps),
+                 as.integer(nsnps(data)),
+                 as.integer(nids(data)),
+                 as.character(coding(data)),
+                 as.character(pedfilename),
+                 as.logical(export012na))
+  }
+}