eSetFilter {genefilter}R Documentation

A function to filter an eSet object

Description

Given a Bioconductor's eSet object, this function filters genes using a set of selected filters.

Usage

eSetFilter(eSet)
getFilterNames()
getFuncDesc(lib = "genefilter", funcs = getFilterNames())
getRdAsText(lib)
parseDesc(text)
parseArgs(text)
showESet(eSet)
setESetArgs(filter)
isESet(eSet)

Arguments

eSet eSet an eSet object
lib lib a character string for the name of an R library where functions of interests reside
funcs funcs a vector of character strings for names of functions of interest
text text a character of string from a filed (e. g. description, argument, ..) filed of an Rd file for a fucntion
filter filter a character string for the name of a filter function

Details

A set of filters may be selected to filter genes in through each of the filters in the order the filters have been selected

Value

A logical vector of length equal to the number of rows of 'expr'. The values in that vector indicate whether the corresponding row of 'expr' passed the set of filter functions.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functonalities through R

Author(s)

Jianhua Zhang

See Also

genefilter

Examples

  if(interactive()){
      library("genefilter", character.only = TRUE)
      library("Biobase", character.only = TRUE)
      data(geneData)
      data(geneCov)
      covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3")
      names(covdesc) <- names(geneCov)
      pdata <- new("phenoData", pData=geneCov, varLabels=covdesc)
      eset <- new("exprSet", exprs=geneData, phenoData=pdata)

      res <- eSetFilter(eset)
  }

[Package genefilter version 1.8.0 Index]