predictFromAlignment: Predict sift scores from a protein alignment

In omarwagih/siftr: generate SIFT scores directly in R

Description

Predict sift scores from a protein alignment

Usage

predictFromAlignment(aln, cores = 1)

Arguments

aln	path to alignment file in fasta format or character vector of protein sequences
cores	number of cores for parallel processing (default: 1)

Value

matrix of sift scores

Examples

# Generate dummy alignment
aln = c('SSSS', 'STTT', 'SYSY', 'ASST', 'KKHS')

# Generate matrix of sift scores
sift_mat = predictFromAlignment(aln)

# Show summary of run
summary(sift_mat)

# Convert to data frame and filter out unreliable predictions
sift_df = filterPredictions(sift_mat, score_thresh = 0.05, residue_thresh = 2)

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