parseDB: Parse a .fasta Database

Description Usage Arguments Details Value Author(s) Examples

Description

parseDB() parses a .fasta database from Uniprot into a data table containing each protein accession ID in one column and the protein sequence in another column.

Usage

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parseDB(database)

Arguments

database

a .fasta database downloaded from Uniprot.

Details

databases must be downloaded from Uniprot or they may not work. File extension of database should be changed from ".fasta" to ".txt" prior to use. This function was built to organize .fasta databases for easier manipulation in R (such as prior to input into the phindPhospho() function) or other analysis software.

Value

a data table with two columns: protein accession ID and protein sequence

Author(s)

Jacob M. Wozniak (jakewozniak@gmail.com)

Examples

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require(PhosPhinder)

examples.path = system.file("extdata", package = "PhosPhinder")
uniprot_ref.path = paste(examples.path, "/Human_Uniprot_Example.txt", sep="")

uniprot_ref = readLines(uniprot_ref.path)

parseDB_Example <- parseDB(uniprot_ref)

filename1 <- paste(examples.path, "/Human_Uniprot_Parsed_", Sys.Date(), ".txt", sep="")

write.table(parseDB_Example, filename1, row.names=FALSE, col.names=FALSE, sep="\t")

jmwozniak/PhosPhinder documentation built on May 30, 2019, 1:32 p.m.