genefilter {genefilter} | R Documentation |
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
.
genefilter(expr, flist)
expr |
A matrix or exprSet that the filter functions will be
applied to. |
flist |
A list of filter functions to apply to the array. |
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.
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.
R. Gentleman
set.seed(-1) f1 <- kOverA(5, 10) flist <- filterfun(f1, allNA) exprA <- matrix(rnorm(1000, 10), nc=10) ans <- genefilter(exprA, flist)