extract_pondrFIT: Extract data from URLs produced by PONDR-FIT meta-predictor

In vanbibn/mineDisProt: Mine/Extract data on protein disorder from DisProt (and other databases)

Description

This function extracts the relevant data from the temporaty URL produced by analyzing a protein sequence in the PONDR-FIT protein disorder meta-predictor (http://original.disprot.org/pondr-fit.php). It then calculates average and percent disorder scores from the per-residue scores. Before using this function, URLs should be collected and put in a '.csv' file with the UniProt ID in the first column and URL in the second.

Usage

extract_pondrFIT(path, save_raw = NULL, output = NULL)

Arguments

path	A character string desctibing the path to the csv file containing URLs to be read.
save_raw	A character string describing the path to a *Directory* where intermediate files for each protein should be saved. If 'NULL', the intermediate files will not be written to csv.
output	A character string describing the path to write the output data frame. If 'NULL', an output file will not be written.

Value

A data frame containing the average disorder scores, percent disorder scores, and length (in addition to the UniProt ID and URL that were input).

Examples

# extract_pondrFIT("inst/extdata/pondrfit-url.csv")
# extract_pondrFIT("data/pondrfit-url.csv", save_raw = NULL, output = "data/PONDR-FIT.csv")

vanbibn/mineDisProt documentation built on April 30, 2020, 1:39 p.m.