R/transposeToSubjectLayout.R

In TNO/PhenotypeDatabase-RUtils: R package with utility functions for GSCF.

# Robert Ernst/Jordy Coolen
# Transpose transcriptomics files to subject layout

# Copyright 2013 Robert Ernst/Jordy Coolen
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
# http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

## Example input file 
## Feature  Time  Subject_1 Subject_2
## 58812    5w    2.34      3.12
## 500012   5w    5.123     12.12

## Example output file 
## Feature    58812   500012
## Time       5w      5w
## Subject_1  2.34    5.123
## Subject_2  3.12    12.12

require(gdata)

transposeToSubjectLayout <- function
### transpose transcriptomics files to subject layout.
(filename, ##<< excel filename
 dataPath ##<< path to excel filename
){
  options(digits=22)
  
  ## Defining the results folder
  outputDir=paste0(dataPath,"results/")
  
  # Create output folder
  system(paste0("mkdir ",outputDir))
  
  #read tab delimited file
  data = read.table(paste0(dataPath,filename),header=F,sep ="\t",quote="\"'",dec=".",check.names=FALSE, stringsAsFactors=F)
  
  filename = gsub(x=filename,".txt","_transposeddata.txt")
  
  dataTransposed = t(data) #transpose data
  
  #Save transposed tab delimited output
  write.table(dataTransposed, file=paste0(outputDir,filename), quote = FALSE, sep='\t', row.names = FALSE, col.names= FALSE)
  
  ### Return transposed data.matrix
}