gapFilter: A filter to select genes based on there being a gap.

In Bioconductor/genefilter: genefilter: methods for filtering genes from high-throughput experiments

A filter to select genes based on there being a gap.

Description

The gapFilter looks for genes that might usefully discriminate between two groups (possibly unknown at the time of filtering). To do this we look for a gap in the ordered expression values. The gap must come in the central portion (we exclude jumps in the initial Prop values or the final Prop values). Alternatively, if the IQR for the gene is large that will also pass our test and the gene will be selected.

Usage

gapFilter(Gap, IQR, Prop, na.rm=TRUE, neg.rm=TRUE)

Arguments

Gap	The size of the gap required to pass the test.
IQR	The size of the IQR required to pass the test.
Prop	The proportion (or number) of samples to exclude at either end.
na.rm	If TRUE then NA's will be removed before processing.
neg.rm	If TRUE then negative values in x will be removed before processing.

Details

As stated above we are interested in

Value

A function that returns either TRUE or FALSE depending on whether the vector supplied has a gap larger than Gap or an IQR (inter quartile range) larger than IQR. For computing the gap we want to exclude a proportion, Prop from either end of the sorted values. The reason for this requirement is that genes which differ in expression levels only for a few samples are not likely to be interesting.

Author(s)

R. Gentleman

See Also

ttest, genefilter

Examples

 set.seed(256)
 x <- c(rnorm(10,100,3), rnorm(10, 100, 10))
 y <- x + c(rep(0,10), rep(100,10))
 tmp <- rbind(x,y) 
 Gfilter <- gapFilter(200, 100, 5)
 ffun <- filterfun(Gfilter)
 genefilter(tmp, ffun)

Bioconductor/genefilter documentation built on Feb. 4, 2024, 11:20 a.m.