PARSE RTCA OUTPUT FILE

Description

The function parses RTCA output file into RTCA object

Usage

parseRTCA(file, dec = ".", phenoData, maskWell, ...)

Arguments

Details

A csv-like format file can be exported from the RTCA device, which can be fed into this function to set up an instance of RTCA object.

In the /extdata/ directory of the package, such a file is provided as an example. The first line contains the experiment ID, which is followed by a matrix of recorded data in the tabular form. The first and second column records the time-interval in the unit of hour and hour-minute-second format respectively. The rest columns then record the read-out (‘Cell-Index’, or ‘CI’) of the device, with each well a role.

phenoData allows user to annotate the wells.Its usage mimicks the ExpressionSet object in the Biobase package.

maskWell allows to mask wells in case, for example, they are known to be contaminated. The values can be either a vector of well names, or a regular expression pattern for wells to be masked. To learn regular expression patterns see grep.

Value

An object of RTCA-class

Author(s)

Jitao David Zhang jitao_david.zhang@roche.com

References

http://www.roche-applied-science.com/proddata/gpip/3_8_9_1_1_1.html

Examples

require(RTCA)
  
ofile <- system.file("extdata/testOutput.csv", package="RTCA")
pfile <- system.file("extdata/testOutputPhenoData.csv", package="RTCA")

pData <- read.csv(pfile, sep="\t", row.names="Well")
metaData <- data.frame(labelDescription=c(
"Rack number",
"siRNA catalogue number",
"siRNA gene symbol",
"siRNA EntrezGene ID",
"siRNA targeting accession"
))

phData <- new("AnnotatedDataFrame", data=pData, varMetadata=metaData)
x <- parseRTCA(ofile, phenoData=phData)

print(x)

## mask wells, e.g. due to unusual values
x.skip <- parseRTCA(ofile, phenoData=phData, maskWell=c("D09"))
x.skip.multiWells <- parseRTCA(ofile, phenoData=phData, maskWell=c("A01", "B01",
"C02"))
## skip the last row
x.skip.pattern <- parseRTCA(ofile, phenoData=phData,
maskWell=c("H[0-9]{2}"))

## check the number of masked wells
noMasked <- function(x) sum(apply(x, 2, function(x) all(is.na(x))))
noMasked(exprs(x))
noMasked(exprs(x.skip))
noMasked(exprs(x.skip.multiWells))
noMasked(exprs(x.skip.pattern))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RTCA)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCA/parseRTCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: parseRTCA
> ### Title: PARSE RTCA OUTPUT FILE
> ### Aliases: parseRTCA
> ### Keywords: IO file
> 
> ### ** Examples
> 
> require(RTCA)
>   
> ofile <- system.file("extdata/testOutput.csv", package="RTCA")
> pfile <- system.file("extdata/testOutputPhenoData.csv", package="RTCA")
> 
> pData <- read.csv(pfile, sep="\t", row.names="Well")
> metaData <- data.frame(labelDescription=c(
+ "Rack number",
+ "siRNA catalogue number",
+ "siRNA gene symbol",
+ "siRNA EntrezGene ID",
+ "siRNA targeting accession"
+ ))
> 
> phData <- new("AnnotatedDataFrame", data=pData, varMetadata=metaData)
> x <- parseRTCA(ofile, phenoData=phData)
Read 245 items
> 
> print(x)
Experiment ID: 0811171136P1 
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2016-07-02 23:50:56 

ExpressionSet (storageMode: lockedEnvironment)
assayData: 242 features, 96 samples 
  element names: exprs 
protocolData: none
phenoData
  rowNames: A01 A02 ... H12 (96 total)
  varLabels: Rack CatalogNumber ... Accession (5 total)
  varMetadata: labelDescription
featureData
  featureNames: 0 0.93 ... 90.33 (242 total)
  fvarLabels: timepoints
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> 
> ## mask wells, e.g. due to unusual values
> x.skip <- parseRTCA(ofile, phenoData=phData, maskWell=c("D09"))
Read 245 items
> x.skip.multiWells <- parseRTCA(ofile, phenoData=phData, maskWell=c("A01", "B01",
+ "C02"))
Read 245 items
> ## skip the last row
> x.skip.pattern <- parseRTCA(ofile, phenoData=phData,
+ maskWell=c("H[0-9]{2}"))
Read 245 items
> 
> ## check the number of masked wells
> noMasked <- function(x) sum(apply(x, 2, function(x) all(is.na(x))))
> noMasked(exprs(x))
[1] 0
> noMasked(exprs(x.skip))
[1] 1
> noMasked(exprs(x.skip.multiWells))
[1] 3
> noMasked(exprs(x.skip.pattern))
[1] 12
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>