annotFilter {mdgsa} | R Documentation

## Checks and filters an annotation list.

### Description

Checks that the annotated genes (those in the annotation list) are consistent with the universe of genes defined by the ranking index. Filters out functional blocks too 'big' or too 'small'.

### Usage

    annotFilter(annot, index, minBlockSize = 10, maxBlockSize = 500,
      verbose = TRUE)

### Arguments

`annot` | an annotation list.
`index` | ranking index. Vector, matrix or data.frame
`minBlockSize` | minimum block size kept
`maxBlockSize` | maximum block size kept
`verbose` | verbose

### Details

`index` is optional. When it is not provided, the annotation lists is just filtered out by the sizes of the blocks of genes defined in the list.

If a ranking index is provided its names are assumed to be the universe of genes under study. The genes in the annotation list are compared against those of the ranking index and the ones not belonging to the universe are removed out form the annotation in order to compute the size of each functional block. Then the list is filtered by sizes; too big and too small blocks are removed.

No transformation is done over the ranking index or its names (gene IDs).

`index` may just be a character vector containing the names of the genes in the universe, that is, the names or row names of the ranking index.

### Value

a filtered annotation list.

### Author(s)

David Montaner dmontaner@cipf.es

### See Also

`annotMat2list`

### Examples

    rindex <- 1:10
    names (rindex) <- paste ("gene", rindex, sep = "")
    rindex

    annot <- list (paste ("gene", 1:2, sep = ""),          ##too small block
                   paste ("gene", 1:6, sep = ""),          ##right size
                   paste ("gene", 1:5, sep = ""),          ##too big block
                   paste ("gene", c(1:3, 1:3), sep = ""))  ##duplicated IDs
    annot[[2]][1] <- NA
    annot[[2]][2] <- ""
    annot[[2]][3] <- "BAD_ID"
    annot

    annotFilter (annot, minBlockSize = 3, maxBlockSize = 5)
    annotFilter (annot, rindex, minBlockSize = 3, maxBlockSize = 5)

[Package mdgsa version 1.14.0 Index]