filterPredictions: Convert siftr matrix to data frame and filter out unreliable...

In omarwagih/siftr: generate SIFT scores directly in R

Description

Convert siftr matrix to data frame and filter out unreliable predictions. For more information on the filtering see http://sift.bii.a-star.edu.sg/www/SIFT_help.html

Usage

filterPredictions(sift_mat, score_thresh = 0.05, ic_thresh = 3.25,
  residue_thresh = 2)

Arguments

sift_mat	siftr matrix generated using predictFromAlignment
score_thresh	sift score threshold, scores above this threshold are removed (default: 0.05)
ic_thresh	information content threshold, predictions in positions that have an ic above this threshold are considered low confidence and removed (default: 3.25)
residue_thresh	minimum number of aligned residues at the position of prediction (default: 2)

Value

data frame of predictions

omarwagih/siftr documentation built on May 24, 2019, 1:50 p.m.