filterData: filterData

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

Function that filter data and create a report file.

Usage

filterData(expres, controls = NULL, removeNAs = FALSE,
  entrezs = NULL, bySignal = TRUE, signalThr, grups = NULL,
  sigFun.Name = "filt.by.signal", sigThr.as.perc = TRUE,
  byVar = TRUE, variabilityThr, varFun.Name = "sdf",
  varThr.as.perc = TRUE, pairingFun.Name = NULL, targets,
  doReport = NULL, outputDir = NULL, filteringReportFName = NULL)

Arguments

expres	Data set to be filtered.
controls	Vector that indicates wich observations are controls.
removeNAs	If TRUE the Na's observations will be deleted.
entrezs	Name of the file for Entrez genes.
bySignal	If TRUE the data is filtered by signal value.
signalThr	Threshold for filter the data.
grups	Name of the different groups of the data.
sigFun.Name	????????
sigThr.as.perc	???????????
byVar	If TRUE the data is filtered by ?????
variabilityThr	Threshold for filter the data.
varFun.Name	????????
varThr.as.perc	Threshold variability as percentage
pairingFun.Name	Name of the function to be imported to pair data
targets	Name of the targets file.
doReport	If TRUE a report is created.
outputDir	Path of the file created.
filteringReportFName	Name of the report file.

Value

Matrix object with te data filtered

Examples

## Not run: 
load("./ResultsDir/normalizedData.Rda")
repes <- duplicated(exprs(my.norm), MARGIN = 1)
exprs(my.norm) <- exprs(my.norm)[!repes, ]
eset_norm <- my.norm
load("./ResultsDir/controls.Rda")
removeNAs <- TRUE
load("./ResultsDir/Entrezs.Rda")
entrezs <- entrezTable
SignalFilter <- TRUE
signalThreshold <- 50
signalFilter.Function <- "filt.by.Signal"
signalThreshold.as.percentage <- TRUE
VarFilter <- TRUE
variabilityThreshold <- 50
variability.Function <- "sdf"
variabilityThreshold.as.percentage <- TRUE
pairing.Function <- NULL
my.targets <-read.AnnotatedDataFrame("./celfiles/targets.txt", header = TRUE, row.names = 1)
doReport <- TRUE
outputDir <- "./ResultsDir"
FilteringReportFileName <- "FilteringReport.txt"

exprs.filtered <- filterData(expres = exprs(eset_norm) ,controls = names(controlsTable),
                             removeNAs = TRUE, entrezs = entrezs, bySignal = SignalFilter,
                             signalThr = signalThreshold, grups = pData(eset_norm)$grupo,
                             sigFun.Name = signalFilter.Function,
                             sigThr.as.perc = signalThreshold.as.percentage, byVar = VarFilter,
                             variabilityThr = variabilityThreshold,
                             varFun.Name = variability.Function,
                             varThr.as.perc = variabilityThreshold.as.percentage,
                             pairingFun.Name = pairing.Function,
                             targets = my.targets, doReport = doReport, outputDir = outputDir,
                             filteringReportFName = FilteringReportFileName)

## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.