Variant set enrichment (VSE) analysis.

Description

The VSE method tests the enrichment of an AVS for a particular trait in a genomic annotation.

Usage

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avs.vse(object, annotation, maxgap=0, pValueCutoff=0.05, boxcox=TRUE, 
lab="annotation", glist=NULL, minSize=100, verbose=TRUE)

Arguments

object

an object. When this function is implemented as the S4 method of class AVS-class, this argument is an object of class 'AVS'.

annotation

a data frame with genomic annotations listing chromosome coordinates to which a particular property or function has been attributed. It should include the following columns: <CHROM>, <START>, <END> and <ID>. The <ID> column can be any genomic identifier, while values in <CHROM> should be listed in ['chr1', 'chr2', 'chr3' ..., 'chrX']. Both <START> and <END> columns correspond to chromosome positions mapped to the human genome assembly used to build the AVS object (see avs.preprocess).

maxgap

a single integer value specifying the max distant (bp) between the AVS and the annotation used to compute the enrichment analysis.

pValueCutoff

a single numeric value specifying the cutoff for p-values considered significant.

boxcox

a single logical value specifying to use Box-Cox procedure to find a transformation of the null that approaches normality (when boxcox=TRUE) or not (when boxcox=FALSE). See powerTransform and bcPower.

lab

a single character value specifying a name for the annotation dataset (this option is overrided if 'glist' is used).

glist

an optional list with character vectors mapped to the 'annotation' data via <ID> column. This option can be used to run a batch mode for gene sets and regulons.

minSize

if 'glist' is provided, this argument is a single integer or numeric value specifying the minimum number of elements for each gene set in the 'glist'. Gene sets with fewer than this number are removed from the analysis.

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Author(s)

Mauro Castro

See Also

AVS-class

Examples

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## Not run: 
#This example requires the RTNdata package! (currently available under request)
library(RTNdata.LDHapMap.rel27)
data(bcarisk)
avs <- new("AVS", markers=bcarisk)
avs <- avs.preprocess(avs, nrand=100)
avs.get(avs)

## End(Not run)

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