genefilter {genefilter}R Documentation

A function to filter genes.

Description

genefilter filters genes in the array expr using the filter functions in flist. It returns an array of logical values (suitable for subscripting) of the same length as there are rows in expr. For each row of expr the returned value is TRUE if the row passed all the filter functions. Otherwise it is set to FALSE.

Usage

genefilter(expr, flist)

Arguments

expr A matrix or exprSet that the filter functions will be applied to.
flist A list of filter functions to apply to the array.

Details

This package uses a very simple but powerful protocol for filtering genes. The user simply constructs any number of tests that they want to apply. A test is simply a function (as constructed using one of the many helper functions in this package) that returns TRUE if the gene of interest passes the test (or filter) and FALSE if the gene of interest fails.

The benefit of this approach is that each test is constructed individually (and can be tested individually). The tests are then applied sequentially to each gene. The function returns a logical vector indicating whether the gene passed all tests functions or failed at least one of them.

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)

R. Gentleman

See Also

genefilter, kOverA

Examples

   set.seed(-1)
   f1 <- kOverA(5, 10)
   flist <- filterfun(f1, allNA)
   exprA <- matrix(rnorm(1000, 10), nc=10)
   ans <- genefilter(exprA, flist)

[Package genefilter version 1.8.0 Index]