phindPhospho: Localize Phospho-sites from Phospho-proteomic Data

In jmwozniak/PhosPhinder: An R package for phospho-site localization and motif extraction from phospho-proteomic datasets

Description

phindPhospho() uses phospho-peptide information to localize the phospho-sites in the full-length protein and returns flanking sequences for subsequent use with tools such as motif-x.

Usage

phindPhospho(data_table, reference_table)

Arguments

data_table	a data table containing your experimentally acquired phospho-peptide data. See "phindPhospho_Input_Example.csv" for an example.
reference_table	a data table containing full protein sequence information for the phospho-peptides in the data_table. This input can be created from any Uniprot database using the parseDB() function. See "Human_Uniprot_Parsed_Example.txt" for an example.

Details

input files must contain the following 5 columns (exactly as below - see "phindPhospho_Input_Example.csv"):

1) Protein_ID - Uniprot accession of protein

2) Peptide_Seq - peptide sequence containing phospho-site(s)

3) Total_Sites - total number of phospho-site(s) within phospho-peptide

4) Phos_Locs - location of phospho-site(s) within phospho-peptide in the ptmRS convention. Multiple phospho-sites should be separated by a semi-colon (eg. "S9(Phospho): 98.56; S18(Phospho): 99.84")

5) Qualifier - unique qualifier of phospho-peptide

Value

a data table with 7 columns:

1) Protein ID - see above

2) Qualifier - see above

3) Pep_Loc - location(s) of phosphosite(s) on peptide

4) Prot_Loc - location(s) of phosphosite(s) on protein

5) Flank_Seq - flanking sequence(s) of phosphosite(s)

6) Confidence - ambiguity of localized phosphosite(s)

7) Prot_Seq - protein sequence

Author(s)

Jacob M. Wozniak ([e-mail])

Examples

examples.path = system.file("extdata", package = "PhosPhinder")
phos_data.path = paste(examples.path, "/phindPhospho_Input_Example.csv", sep="")
parsed_ref.path = paste(examples.path, "/Human_Uniprot_Parsed_Example.txt", sep="")

phos_data <- read.csv(phos_data.path, header=TRUE, row.names = NULL, stringsAsFactors = FALSE)

parsed_ref <- read.table(parsed_ref.path, header=FALSE, row.names=NULL, sep="\t")

phindPhospho_Example <- phindPhospho(phos_data, parsed_ref)

fileName3 <- paste(examples.path, "/PhosPhound_", Sys.Date(), ".txt", sep="")

write.table(phindPhospho_Example, fileName3, row.names=FALSE, append = FALSE,  sep = "\t")

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