genefilter: 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 ExpressionSet that the filter functions will be applied to.

flist

A list of filter functions to apply to the array.

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.

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.

Users can construct their own filters. These filters should accept a vector of values, corresponding to a row of the expr object. The user defined function should return a length 1 logical vector, with value TRUE or FALSE. User-defined functions can be combined with filterfun, just as built-in filters.

Examples

Run this code

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