parseRTCA: PARSE RTCA OUTPUT FILE

In RTCA: Open-source toolkit to analyse data from xCELLigence System (RTCA)

Description

The function parses RTCA output file into RTCA object

Usage

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

Arguments

file	character, name of the RTCA output file
dec	decimal sign of the file
phenoData	phenoData
maskWell	character, either names or regular expression pattern(s) for well(s) to mask
...	other parameters passed to read.table

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 [e-mail]

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))

RTCA documentation built on Nov. 8, 2020, 7:52 p.m.