[Genabel-commits] r797 - pkg/GenABEL/R

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

Author: lckarssen
Date: 2011-10-19 17:52:50 +0200 (Wed, 19 Oct 2011)
New Revision: 797

Added:
   pkg/GenABEL/R/minimac2databel.R
Log:
Added a conversion function minimac2databel() to GenABEL that converts
dose files as created by minimac to DatABEL (filevector) format. This
function is heavily based on mach2databel().




Added: pkg/GenABEL/R/minimac2databel.R
===================================================================
--- pkg/GenABEL/R/minimac2databel.R	                        (rev 0)
+++ pkg/GenABEL/R/minimac2databel.R	2011-10-19 15:52:50 UTC (rev 797)
@@ -0,0 +1,85 @@
+#'
+#' converts Minimac-imputed files to DatABEL (filevector) format
+#'
+#' This function converts Minimac-imputed files to \code{DatABEL} (filevector) format.
+#' After conversion, two files (outfile.fvi and outfile.fvd), corresponding
+#' to single filevector object, will appear on the disk; a 'databel-class'
+#' object connected to these files will be returned to R.
+#' This function is based on mach2databel().
+#'
+#' Note that the last part where the dimnames are altered is related
+#' to our dataset.
+#'
+#' @param imputedgenofile Minimac dose file name
+#' @param infofile Minimac info file name
+#' @param outfile output file name
+#' @param cachesizeMb cache size for the resulting 'databel-class'
+#' object (gets passed directly to the \code{text2databel()} function)
+#'
+#' @return databel-class object
+#'
+#' @author L.C. Karssen
+#'
+#' @keywords IO manip
+#'
+#'
+
+
+minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
+{
+  if (!require(DatABEL))
+    stop("This function requires DatABEL package to be installed")
+  if (missing(imputedgenofile))
+    stop("A dose file must be specified")
+  if (missing(outfile)) outfile <- imputedgenofile
+  ## extract snp names (varnames)
+  tmpname <- ""
+  if (!missing(infofile))
+    {
+      tmp <- scan(infofile, what="character", skip=1)
+      tmp <- tmp[c(T,F,F,F,F,F,F,F,F,F,F,F,F)]
+      ##print(tmp[1:10])
+      tmpname <- get_temporary_file_name()
+      write(tmp, file=tmpname)
+      rm(tmp);gc()
+    } else
+  warning("info file not specified, you will not be able to use snp names (only index)")
+
+  if (tmpname != "")
+    dfaobj <- text2databel(infile=imputedgenofile,
+                           outfile=outfile,
+                           colnames=tmpname,
+                           rownames=1,
+                           skipcols=2,
+                           transpose=FALSE,
+                           R_matrix=FALSE,
+                           type="FLOAT",
+                           readonly=FALSE,
+                           cachesizeMb=cachesizeMb)
+  else
+    dfaobj <- text2databel(infile=imputedgenofile,
+                           outfile=outfile,
+                           rownames=1,
+                           skipcols=2,
+                           transpose=FALSE,
+                           R_matrix=FALSE,
+                           type="FLOAT",
+                           readonly=FALSE,
+                           cachesizeMb=cachesizeMb)
+
+  ## "Normalise" the dimnames
+  dnames <- get_dimnames(dfaobj)
+  subjs <- dnames[[1]]
+  # print(subjs[1:10])
+  subjs <- sub("->", "_", subjs)
+  # print(subjs[1:10])
+  # print(dim(dfaobj))
+  # print(length(subjs))
+  dimnames(dfaobj) <- list(subjs,dnames[[2]])
+
+  if (tmpname != "") {
+    unlink(paste(tmpname, "*", sep=""))
+  }
+
+  return(dfaobj)
+}