read.Data: Read and Annotate RPPA rawdata

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Read and Annotate RPPA rawdata

Description

reads sampledescription and slidedescription txt files and annotates the median expression value in GenePix result files stored in current working directory.

Usage

   read.Data(blocksperarray = 4, spotter = "arrayjet", writetable = FALSE,
   printFlags=FALSE,fileName="Flagged_spots.csv", remove_flagged=NULL, ...)

Arguments

blocksperarray	Integer describing the number of blocks in one array.
spotter	character strings: default arrayjet or aushon.
writetable	logical. If true data are exported as tab delimited text files to current working directory
printFlags	logical. If true flagged spots will exported as csv file
fileName	character string naming the csv file for the flagged spots
remove_flagged	Either NULL or an integer. If an integer, looks into column Flags of the gpr file and removes samples with flag value less than or equal -remove_flagged from the data tables.
...	any other arguments passed to read.gpr

Details

This function reads and annotates RPPA rawdata provided in three different kind of files. It is very important that these data files are in a correct format and stored in the same folder.

The file sampledescription.txt has to be a tab delimited text file with at least 6 columns named plate, column, row, sample_type, sample, concentration and in case of serially diluted samples a column dilution is required. The first 3 columns are describing the location of the sample in the source well plate. The 4th column describes the for different types of samples: measurement, control, neg_control or blank. In the column sample any character string describing the sample is possible. The column concentration has to contain only numerical values. Columns with further phenodata can be added.

The slidedescription.txt describes the array properties. Required columns are: gpr (describing the name of the corresponding gpr file), the columns pad, slide, incubation_run, spotting_run containing integers are generating a unique array identifier. The column target describes the analyzed target and AB_ID the used antibody. Column with further feature data can be added.

The third kind of files are the gpr files as results from image analysis software GenePix using the galfile from a aushon or arrayjet spotter.

Value

expression	matrix with protein expression data
background	matrix with background data
arraydescription	data frame with feature data
sampledescription	data frame with pheno data

Author(s)

Heiko Mannsperger <[e-mail]>

Examples

## Not run: 
  library(RPPanalyzer)
  
  
  dataDir <- system.file("extdata", package="RPPanalyzer")
  setwd(dataDir)
  rawdata <- read.Data(blocksperarray=12, spotter="aushon", printFlags=FALSE, remove_flagged=NULL)
  print(dim(rawdata$expression))
  
  rawdata <- read.Data(blocksperarray=12, spotter="aushon", printFlags=FALSE, remove_flagged=50)
  print(dim(rawdata$expression))
  
## End(Not run)
  
  

RPPanalyzer documentation built on Aug. 28, 2023, 5:07 p.m.