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Last data update: 2014.03.03

R: A function to filter an eSet object

eSetFilter

R Documentation

A function to filter an eSet object

Description

Given a Bioconductor's ExpressionSet 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 ExpressionSet 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.

Author(s)

Jianhua Zhang

Examples

 if( interactive() ) {
   data(sample.ExpressionSet)      
   res <- eSetFilter(sample.ExpressionSet)
 }

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(genefilter)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genefilter/eSetFilter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: eSetFilter
> ### Title: A function to filter an eSet object
> ### Aliases: eSetFilter getFilterNames getFuncDesc getRdAsText parseDesc
> ###   parseArgs setESetArgs isESet showESet
> ### Keywords: manip
> 
> ### ** Examples
> 
> # if( interactive() ) {
>    data(sample.ExpressionSet)      
Warning message:
In data(sample.ExpressionSet) : data set 'sample.ExpressionSet' not found
>    res <- eSetFilter(sample.ExpressionSet)
Loading required package: tkWidgets
Error in eSetFilter(sample.ExpressionSet) : 
  eSetFilter requires the tkWidgets package. Please have it installed
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tkWidgets'
Execution halted