snpDist: Generating a graphic output of the frequency of nsSNPs for...

In a-albuquerque/snpCYP: Assessing potential snp impact on CYP cathalitic activity

Description

This function generates a graphic output of the frequency of nsSNPs for each sequential group of 50 aminoacids at the CYP isoform provided. baseSeqs.rda or a custom sequence of wild isoforms must be loaded.

Usage

snpDist(CYP, seq)

Arguments

CYP	CYP isoform to be analyzed, string
seq	Aminoacid sequence (one-letter code) for the CYP isoform to be analyzed (list of strings)

Value

Visualization of the frequency of nsSNPs for each protein region Also return the SNPs positions for each region

Examples

## Not run: 
load(file = "./data/baseSeqs.rda")
snpDist("CYP1A2",
       paste("AALSQSVPFSATELLLASAIFCLVFWVLKGLRPRVPKGLKSPPEPWGWPLLGHVLTLGKN",
             "LALALSRMSQRYGDVLQIRIGSTPVLVLSRLDTIRQALVRQGDDFKGRPDLYTSTLITDG",
             "TFSTFSTDSGPVWAARRRLAQNALNTFSIASDPASSSSCYLEEHVSKEAKALISRLQELM",
             "GHFGHFDPYNQVVVSVANVIGAMCFGQHFPESSDEMLSLVKNTHEFVETASSGNPLDFFP",
             "PNPALPNPALQRFKAFNQRFLWFLQKTVQEHYQKNSKNSVRDITGALFKHSKKGPRASGN",
             "PQPQEKIVNLVNDIFGAGFDTVTTAISWSLMYLVTKPEIQRKIQKELDTVIGRERRPRLS",
             "PQPQLPYLEAFILETFRHSSFLPFTIPHSTTRDTTLNGFYIPKKCCVFVNQWQVNHDPEL",
             "EEDPSEFRPERFLTADGTAINKPLSEKMMLFGMGKRRCIGEVLAKWEIFLFLAILLQQLE",
             "SSVPPGVKVDLTPIYGLTMKHARCEHVQARLRFSIN", sep=""))
 
## End(Not run)

a-albuquerque/snpCYP documentation built on Dec. 18, 2021, 9:23 p.m.