Description Usage Arguments Details Value Author(s) Examples
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.
1 | parseDB(database)
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database |
a .fasta database downloaded from Uniprot. |
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.
a data table with two columns: protein accession ID and protein sequence
Jacob M. Wozniak (jakewozniak@gmail.com)
1 2 3 4 5 6 7 8 9 10 11 12 | 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")
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