crossReferenceList: crossReferenceList

In MichelleMengzhi/hmtp: Homology Modeling Templates Preparation

Description

Create a dataframe storing entries and corresponding cross reference. There might be more than one pdb names for one sequence, the package only pick the last one in given file.

Usage

crossReferenceList(crossReferenceFile, mySubjectClass)

Arguments

crossReferenceFile	The filepath of sequence database whose sequences have pdb in text.
mySubjectClass	A S4 class storing all information from the given sequence database in fasta.

Value

A dataframe with column "entry", "crossReference" which stores entry names and their corresponding PDB name

Examples

# Go to UniPort, download IPR005814 family entry database in text that is reviewed and has
# 3D structure (databaseExample.fasta, databaseExample.txt).

mySubject <- Biostrings::readAAStringSet("databaseExample.fasta")
crossReferenceList("databaseExample.txt", mySubject)

MichelleMengzhi/hmtp documentation built on Dec. 12, 2019, 12:54 a.m.