extract_tidy_domains_from_xml: extract_tidy_domains_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_domains_from_xml

Description

extract_tidy_domains_from_xml

Usage

extract_tidy_domains_from_xml(xml.document)

Arguments

xml.document

A xml_document downloaded from HMMER.

Value

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

• ienvEnvelope start position

• jenvEnvelope end position

• ialiAlignment start position

• jaliAlignment end position

• biasnull2 score contribution

• oascTOptimal alignment accuracy score

• bitscoreOverall score in bits, null corrected, if this were the only domain in seq

• cevalueConditional E-value based on the domain correction

• ievalueIndependent E-value based on the domain correction

• is_reported1 if domain meets reporting thresholds

• is_included1 if domain meets inclusion thresholds

• alimodelAligned query consensus sequence phmmer and hmmsearch, target hmm for hmmscan

• alimlineMatch line indicating identities, conservation +’s, gaps

• aliaseqAligned target sequence for phmmer and hmmsearch, query for hmmscan

• alipplinePosterior probability annotation

• alihmmnameName of HMM (query sequence for phmmer, alignment for hmmsearch and target hmm for hmmscan)

• alihmmaccAccession of HMM

• alihmmdescDescription of HMM

• alihmmfromStart position on HMM

• alihmmtoEnd position on HMM

• aliMLength of model

• alisqnameName of target sequence (phmmer, hmmscan) or query sequence(hmmscan)

• alisqaccAccession of sequence

• alisqdescDescription of sequence

• alisqfromStart position on sequence

• alisqtoEnd position on sequence

• aliLLength of sequence

Examples

## Not run: 
 xml.path %>%
   read_xml() %>%
   extract_tidy_domains_from_xml()

## End(Not run)

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