check: Checks a GeneSetCollection

In llrs/GSEAdv: Analyze Gene Sets Collections Properites

Description

Checks that all the collection types is the same. Issues a warning when a GOCollection is detected. Checks tat all the geneIdTypes is the same for all the GeneSets. Checks that a GeneSet is bigger or equal to two genes.

Usage

check(object)

## S4 method for signature 'GeneSetCollection'
check(object)

## S4 method for signature 'GeneSetCollection'
geneIdType(object)

## S4 method for signature 'GeneSetCollection'
collectionType(object)

Arguments

object

A GeneSetCollection

Value

A geneSetCollection

Methods (by class)

• GeneSetCollection: Applies the checks

• GeneSetCollection: Returns the geneIdType present in the GeneSetCollection

• GeneSetCollection: Returns the collectionType present in the GeneSetCollection

Examples

isTRUE(check(Info))
data(sample.ExpressionSet)
ai <- AnnotationIdentifier(annotation(sample.ExpressionSet))
geneIds <- featureNames(sample.ExpressionSet)[100:109]
gs3 <- GeneSet(geneIds=geneIds, type=ai,
               setName="sample1", setIdentifier="102")
uprotIds <- c("Q9Y6Q1", "A6NJZ7", "Q9BXI6", "Q15035", "A1X283",
              "P55957")
gs4 <- GeneSet(uprotIds, geneIdType=UniprotIdentifier())
gsc <- GeneSetCollection(list(gs3, gs4))
gsc
check(gsc)
geneIdType(Info)
collectionType(Info)

llrs/GSEAdv documentation built on May 29, 2019, 6 p.m.