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Load UniProt human canonical protein FASTA file

Source: R/gsea.R
load_uniprot_human_fasta.Rd

Load UniProt human canonical protein FASTA file

Usage

load_uniprot_human_fasta(scratchdir = ".")

Arguments

scratchdir

character, directory in which the file from Google Cloud Storage should be downloaded

Value

Biostrings::XStringSet object returned from reading in the FASTA file with Biostrings::readAAStringSet()

Details

The human proteome FATSA for canonical proteins was downloaded from UniProt on 2/3/2021 (UniProtKB query "reviewed:true AND proteome:up000005640").

See also

find_flanks()

Examples

fasta = load_uniprot_human_fasta()
#> 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’
head(fasta)
#> AAStringSet object of length 6:
#>     width seq                                               names               
#> [1]   349 MKGLYFQQSSTDEEITFVFQEKE...YEAKVSMEAVQKNQGRKKQVVQF O95825
#> [2]   694 MTDTVFSNSSNRWMYPSDRPLQS...LKNKDKKIERWHQLQNENHVSSD Q9Y2J0
#> [3]  1077 MDTDSQRSHLSSFTMKLMDKFHS...WELSLKIKPRNITRRKTDREEKT Q13905
#> [4]   716 MEDSTSPKQEKENQEELGETRRP...EAVLLAAENEESEEDEDEEDDYD Q5TD94
#> [5]   442 MALPGARARGWAAAARAAQRRRR...LLTLLPQLQEAWQQRTPSPVPGG Q9HA92
#> [6]    77 MSVAFVPDWLRGKAEVNQETIQR...HRNLIYLATIADASPTSTSKAME Q9UHA2