gapFilter {genefilter} | R Documentation |

## 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)

[Package

*genefilter* version 1.8.0

Index]