checkOverlapDomains: Identify feature type(s) containing overlapped...
In BIONF/PhyloProfile: PhyloProfile

checkOverlapDomains

R Documentation

Identify feature type(s) containing overlapped domains/features

Description

Identify feature type(s) containing overlapped domains/features

Usage

checkOverlapDomains(domainDf)

Arguments

domainDf

input domain dataframe

Value

List of feature types that have overlapped domains

Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

Examples

# get domain data
seedID <- "101621at6656"
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
domainDf <- parseDomainInput(seedID, domainFile, "file")
# get seedDf and orthoDf
subDf <- domainDf[
    domainDf$seedID ==
    "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
# check overlap features
PhyloProfile:::checkOverlapDomains(orthoDf)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.