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Find human flanks

Source: R/gsea.R
find_flanks.Rd

Find flanking sequence in human ortholog of PTM

Usage

find_flanks(x, fasta, type = "uniprot")

Arguments

x

character, human accession for PTM, e.g., "Q96QG7_S548s"

fasta

Biostrings::XStringSet object returned from reading in a human protein FASTA file with Biostrings::readAAStringSet(). Names of the Biostrings::XStringSet object should be set to the human protein accession, e.g., "Q96QG7". Can be the result of load_uniprot_human_fasta(), which returns the version of the Uniprot human protein FASTA used in the manuscript.

type

character, type of accession

Value

character, pipe-separated string of human flanking sequences for the PTM

See also

load_uniprot_human_fasta()

Examples

fasta = load_uniprot_human_fasta(scratchdir="/tmp")
#> Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘RJSONIO’
#> Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘RJSONIO’
x = "Q96QG7_S548s"
find_flanks(x, fasta)
#> [1] "TEDGMQESP______"