[Genabel-commits] r1349 - pkg/GenABEL/R

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

Author: lckarssen
Date: 2013-10-17 16:02:59 +0200 (Thu, 17 Oct 2013)
New Revision: 1349

Modified:
   pkg/GenABEL/R/impute2mach.R
Log:
In GenABEL's impute2mach() function:
- Minor fixes in the documentation
- Some code layout improvements (space after comma, split long lines, F -> FALSE)

No functional changes.


Modified: pkg/GenABEL/R/impute2mach.R
===================================================================
--- pkg/GenABEL/R/impute2mach.R	2013-10-17 12:10:39 UTC (rev 1348)
+++ pkg/GenABEL/R/impute2mach.R	2013-10-17 14:02:59 UTC (rev 1349)
@@ -1,92 +1,109 @@
 #' converts IMPUTE to MACH files
 #'
 #' function to convert IMPUTE files to MACH format
-#' 
+#'
 #' @param genofile IMPUTE genotype file name
 #' @param infofile IMPUTE info file name
 #' @param samplefile IMPUTE sample file name
 #' @param machbasename base name for MACH-formatted outputs
-#' @param maketextdosefile whether text dosefile is to 
-#' be generated (if not, only filevector (*.fvi / *.fvd) files, usable 
-#' with ProbABEL, will be generated)
+#' @param maketextdosefile whether a text dosefile is to
+#' be generated (if not, only filevector (*.fvi / *.fvd) files, usable
+#' with ProbABEL/DatABEL, will be generated). Default: TRUE
 #' @param ... arguments passed to \link{extract.annotation.impute}
-#' (DO CHECK documentation, otherwise your annotation may be 
+#' (DO CHECK the documentation, otherwise your annotation may be
 #' skrewed up!)
-#' 
+#'
 #' @author Yurii Aulchenko
-#' 
+#'
 #' @keywords IO manip
-#' 
+#'
 #' @return nothing returned except files generated on the disk
-#' 
-#' 
+#'
+#'
 
-impute2mach <- function(genofile,infofile,samplefile,machbasename, maketextdosefile = TRUE, ... )
+impute2mach <- function(genofile, infofile, samplefile, machbasename,
+                        maketextdosefile = TRUE, ... )
 {
     if (!require(DatABEL))
         stop("this function requires DatABEL package to be installed")
-    
+
     if (!is.character(machbasename)) stop("machbasename must be character")
+
     if (length(machbasename) == 1) {
-		machdose <- paste(machbasename,".machdose",sep="")
-		machprob <- paste(machbasename,".machprob",sep="")
-		machinfo <- paste(machbasename,".machinfo",sep="")
-        machlegend <- paste(machbasename,".machlegend",sep="")
+        machdose <- paste(machbasename, ".machdose", sep="")
+        machprob <- paste(machbasename, ".machprob", sep="")
+        machinfo <- paste(machbasename, ".machinfo", sep="")
+        machlegend <- paste(machbasename, ".machlegend", sep="")
     } else if (length(machbasename) == 4) {
         if (anyDuplicated(machbasename)) stop("names must be unique")
         machdose <- machbasename[1]
-		machprob <- machbasename[2]
-		machinfo <- machbasename[3]
-		machlegend <- machbasename[4]
+        machprob <- machbasename[2]
+        machinfo <- machbasename[3]
+        machlegend <- machbasename[4]
     } else stop("machbasename must be character of length 1 or 4")
-    
+
     # create temporary DA file
-	
-	#print("before impute2databel");
-    dfo <- impute2databel(genofile=genofile,samplefile=samplefile,outfile=genofile)
-	#print("after impute2databel");
-	
-	#if (maketextdosefile) {
-        #tmpname2 <- get_temporary_file_name()    
+
+      #print("before impute2databel");
+    dfo <- impute2databel(genofile=genofile, samplefile=samplefile, outfile=genofile)
+        #print("after impute2databel");
+
+        #if (maketextdosefile) {
+        #tmpname2 <- get_temporary_file_name()
         # transpose file
-        # ... 
-        #dfo <- as(dfo,"matrix")
+        # ...
+        #dfo <- as(dfo, "matrix")
     #}
     # get annotattion
     #print("calling extract.annotation.impute")
-    annot <- extract.annotation.impute(genofile=genofile,infofile=infofile, ... )
-    #print(annot[1:5,])
-    
+    annot <- extract.annotation.impute(genofile=genofile, infofile=infofile, ... )
+    #print(annot[1:5, ])
+
     # arrange MLINFO and legend file
     #SNP    Al1    Al2    Freq1    MAF    Quality    Rsq
-    annot$MAF <- pmin(annot$Freq1,(1.-annot$Freq1))
-    #print(annot[1:5,])
-    info_annot <- annot[,c("name","A1","A0","Freq1","MAF","Quality","Rsq")]
-    #print(info_annot[1:5,])
-    write.table(info_annot,file=machinfo,row.names=FALSE,col.names=TRUE,quote=F,sep="\t")
-    legend_annot <- annot[,c("name","pos","A1","A0")]
-    #print(legend_annot[1:5,])
-    write.table(legend_annot,file=machlegend,row.names=FALSE,col.names=TRUE,quote=F,sep="\t")
-    
+    annot$MAF <- pmin(annot$Freq1, (1. - annot$Freq1))
+    #print(annot[1:5, ])
+    info_annot <- annot[, c("name", "A1", "A0", "Freq1", "MAF", "Quality", "Rsq")]
+    #print(info_annot[1:5, ])
+    write.table(info_annot, file=machinfo,
+                row.names=FALSE,
+                col.names=TRUE,
+                quote=FALSE,
+                sep="\t")
+    legend_annot <- annot[, c("name", "pos", "A1", "A0")]
+    #print(legend_annot[1:5, ])
+    write.table(legend_annot, file=machlegend,
+                row.names=FALSE,
+                col.names=TRUE,
+                quote=FALSE,
+                sep="\t")
+
     if (maketextdosefile) {
         # arrange MLDOSE file
         ids <- get_dimnames(dfo)[[1]]
         if (file.exists(machdose)) unlink(machdose)
-        outfile <- file(machdose,open="wt")
+
+        outfile <- file(machdose, open="wt")
+
         for (i in 1:dim(dfo)[1])
         {
-            # when using transposed DA object, use as.vector(dfo[,i]) (COLUMN!!!)
-            outline <- c(ids[i],"MLDOSE",as(dfo[i,],"vector"))
+            # when using transposed DA object, use as.vector(dfo[, i]) (COLUMN!!!)
+            outline <- c(ids[i], "MLDOSE", as(dfo[i, ], "vector"))
             #print(outline)
             #print(i)
             #print(class(outline))
-            write(x=outline,file=outfile,append=TRUE,ncolumns=length(outline),sep=" ")
+            write(x=outline, file=outfile,
+                  append=TRUE,
+                  ncolumns=length(outline),
+                  sep=" ")
+
             if ((i %% 100)==0 || i==dim(dfo)[1]) print(i)
         }
         close(outfile)
-        #unlink(paste(tmpname2,"*",sep=""))
+        #unlink(paste(tmpname2, "*", sep=""))
     }
     #print("AAA")
     disconnect(dfo)
-    rm(dfo);gc()
-}
\ No newline at end of file
+    rm(dfo)
+    gc()
+}