mapSequence: Map the Protein Sequence Function

Description Usage Arguments Value Examples

View source: R/mapSequence.R

Description

The function to identify a sequence.

Usage

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mapSequence(query, search = NULL, full_length = FALSE)

Arguments

query

the sequence to be searched, it can be either a string or an AAString object from the Biostrings package

search

argument to choose search strategy. Can be set to 'exact', 'approximate' or 'mixed'. Defaults to 'mixed', meaning first tries to find exact match. If no target can be found, uses approximate search strategy to identify query sequence in database.

full_length

a boolean indicating whether or not for exact matches, the query sequence must be matching the full target sequence. By default, a partial exact match is also reported as exact match.

Value

a data.frame containing the information of matches for the query sequence

Examples

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mapSequence(query='MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')
mapSequence(search='mixed',query='NKLLQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')

klarakaleb/roma documentation built on Nov. 11, 2020, 5:36 a.m.