loadInterProTree: Load the hierarchy of relationships between InterPro's...

In vitkl/ProtDomSeq: Work with InterPro Protein Domains and FASTA Sequences (UniProt)

Description

Load the hierarchy of relationships between InterPro's entries

Usage

loadInterProTree(filename)

Arguments

filename	character, where to download and / or where to find InterPro Entry relationships tree file. Details: https://www.ebi.ac.uk/interpro/download.html
tree	object of class "InterProTree", the output of loadInterProTree function
ParentChildTreeLines	argument for non-exported loadChildrenForLevel: the lines of the InterPro Entry relationships tree file (character)
levels	argument for non-exported loadChildrenForLevel: the mapping between the levels and the lines in ParentChildTreeLines
level	argument for non-exported loadChildrenForLevel: integer, which level to get children for
regex	argument for non-exported loadChildrenForLevel: regex that matches InterProID (IPR[[:digit:]]6)
allchildren	argument for non-exported loadChildrenForLevel: whether to return all children or only a specific level

Value

object of S3 class "InterProTree" containing data.table that provides the mapping between layers, the lines of the InterPro Entry relationships tree file (character) and the mapping between the levels and the lines in ParentChildTreeLines

Author(s)

Vitalii Kleshchevnikov

See Also

readInterProGFF3

Examples

InterProScan_domains_nonred = collapseByInterProID(InterProScan_features = InterProScan_domains, id_col = "Dbxref")

vitkl/ProtDomSeq documentation built on May 3, 2019, 8:08 p.m.