detectSNP: Generating a graphic output of the number of nsSNPs for each...

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

Description

This function generates a graphic output of the number of nsSNPs in each of the following CYP isoforms (if provided): CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4. baseSeqs.rda or a custom sequence of wild isoforms must be loaded.

Usage

detectSNP(CYPs, seqs)

Arguments

CYPs	list of CYPs to be analyzed, list of strings
seqs	Aminoacid sequences in FASTA format, list of strings

Value

Visualization of the amount of snSNPs for each CYP analyzed Also return the SNPs positions for each CYP

Examples

## Not run: 
load(file = "./data/baseSeqs.rda")
detectSNP(list("CYP1A2", "CYP2B6"),
list(paste("ASASQSVPFSATELLLASAIFCLVFWVLKGLRPRVPKGLKSPPEPWGWPLLGHVLTLGKN",
          "PHLALSRMSQRYGDVLQIRIGSTPVLVLSRLDTIRQALVRQGDDFKGRPDLYTSTLITDG",
          "QSLTFSTDSGPVWAARRRLAQNALNTFSIASDPASSSSCYLEEHVSKEAKALISRLQELM",
          "AGPGHFDPYNQVVVSVANVIGAMCFGQHFPESSDEMLSLVKNTHEFVETASSGNPLDFFP",
          "ILRYLPNPALQRFKAFNQRFLWFLQKTVQEHYQDFDKNSVRDITGALFKHSKKGPRASGN",
          "LIPQEKIVNLVNDIFGAGFDTVTTAISWSLMYLVTKPEIQRKIQKELDTVIGRERRPRLS",
          "DRPQLPYLEAFILETFRHSSFLPFTIPHSTTRDTTLNGFYIPKKCCVFVNQWQVNHDPEL",
          "WEDPSEFRPERFLTADGTAINKPLSEKMMLFGMGKRRCIGEVLAKWEIFLFLAILLQQLE",
          "FSVPPGVKVDLTPIYGLTMKHARCEHVQARLRFSIN", sep=""), paste("MEL",
          "SVLLFLALLTGLLLLLVQRHPNTHDRLPPGPRPLPLLGNLLQMDRRGLLKSFLRFRE",
          "KYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNR",
           "WKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIIC",
           "SIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKYFPGAHRQVYKNLQE",
          "INAYIGHSVEKHRETLDPSAPKDLIDTYLLHMEKEKSNAHSENAHQNLNLNTLSLFFAGT",
          "ETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFS",
          "DLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGAL",
          "KKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKI",
          "PPTYQIRFLPR", sep="")))

## End(Not run)

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