extract_tidy_hits_from_xml: extract_tidy_hits_from_xml

In currocam/toolkit4pySCA: A set of useful functions for performing an Statistical Coupling Analysis from scratch in R and using pySCA

extract_tidy_hits_from_xml

Description

extract_tidy_hits_from_xml

Usage

extract_tidy_hits_from_xml(xml.document)

Arguments

xml.document

A xml_document downloaded from HMMER that contain hits.

Value

A tidy data.frame containing available hits' information in xml_document.

• name: Name of the target (sequence for phmmer/hmmsearch, HMM for hmmscan)

• acc: Accession of the target

• acc2: Secondary accession of the target

• id: Identifier of the target

• desc: Description of the target

• score: Bit score of the sequence (all domains, without correction)

• pvalue: P-value of the score

• evalue: E-value of the score

• nregions: Number of regions evaluated

• nenvelopes: Number of envelopes handed over for domain definition, null2, alignment, and scoring.

• ndom: Total number of domains identified in this sequence

• nreported: Number of domains satisfying reporting thresholding

• nregions: Number of regions evaluated

• nincluded: Number of domains satisfying inclusion thresholding

• taxid: The NCBI taxonomy identifier of the target (if applicable)

• species: The species name of the target (if applicable)

• kg: The kingdom of life that the target belongs to - based on placing in the NCBI taxonomy tree (if applicable)

• seqs: An array containing information about the 100% redundant sequences

• pdbs: Array of pdb identifiers (which chains information)

Examples

## Not run: 
read_xml("2abl_A_pdb.xml") %>%
    extract_tidy_hits_from_xml()

## End(Not run)

currocam/toolkit4pySCA documentation built on April 7, 2022, 8:17 p.m.