readInterProGFF3: Read InterProScan output in the gff format, select sequence...

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

Description

Read InterProScan output in the gff format, select sequence features by type

Usage

addInterProEntryTypes(InterProScan_result, entry.list_path)

Arguments

InterProScan_result	GRanges, the output of readInterProGFF3 function
entry.list_path	character, file name and directory where to store InterPro entry list
filename.gz	character, file name and directory to read InterProScan output in the gff format ("./dir/filename.gz")
selected_ENTRY_TYPE	character, select InterPro signature matches from InterProScan_result using these InterPro Entry Types

Details

For further details on the InterProScan output format please visit the link https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats

Value

readInterProGFF3, addInterProEntryTypes or SubsetByInterProEntryType: GRanges-class object containing InterProScan output appended by InterPro Entry Types information, with names metadata and sequence length information imported correctly

getInterProEntryTypes: data.table containing InterPro Entry List ftp://ftp.ebi.ac.uk/pub/databases/interpro/entry.list

getInterPro2memberDB: data.table containing InterProID to member database ID mapping

Author(s)

Vitalii Kleshchevnikov

Examples

# read InterProScan result, download and add InterPro Entry Types information, extract from relevant columns and add names metadata and sequence length information
InterProScan_result = readInterProGFF3("./processed_data_files/all_human_viral_protein_domains.gff3.gz")
InterProScan_result = addInterProEntryTypes(InterProScan_result, "./data_files/entry.list")
# create a subset that contains "Domain", "Active_site", "Binding_site", "Conserved_site", "PTM" signatures
InterProScan_domains = SubsetByInterProEntryType(InterProScan_result)

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