sortDomainsByList: Sort one domain dataframe based on list of ordered feature...
In BIONF/PhyloProfile: PhyloProfile

sortDomainsByList

R Documentation

Sort one domain dataframe based on list of ordered feature types

Description

Sort domain dataframe of one protein based on a given list of ordered feature types

Usage

sortDomainsByList(domainDf = NULL, featureClassOrder = NULL)

Arguments

`domainDf`	domain dataframe
`featureClassOrder`	vector of ordered feature classes

Value

Dataframe contains sorted domain list.

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",]
featureClassOrder <- c("pfam", "smart", "tmhmm", "coils", "signalp", "seg",
    "flps")
# sort
PhyloProfile:::sortDomainsByList(orthoDf, featureClassOrder)

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