extract_pondr: Extract data from text files of protein disorder predictors...

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

Description

This function extracts numerical data from text porduced by the VLXT, VL3, and VSL2 disorder predictors from the Predictor of Natural Disordered Regions (PONDR) website <http://www.pondr.com/>. For each protien sequence, the data from the Raw Output of all three predictors were pasted into a .txt file.

Usage

extract_pondr(directory, output = NULL)

Arguments

directory	A character string describing the path to a Directory where all the text files are located. Note, the function will attempt to read every file in the directory so it should contain only the files you wish to be read.
output	A character string describing the path to write the output matrix. If 'NULL', an output file will not be written.

Value

A matrix containing, for each protein, the Predicted residues ("resid"), Number Disordered Regions ("dis_rgns"), Number residues disordered ("n_dis"), Longest Disordered Region ("lg_rgn"), Overall percent disordered ("pct"), and Average Prediction Score ("avg") for each of the three predictors.

Examples

# extract_pondr("inst/extdata/pondr_text/")

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