SignalpResult_methods: accessor functions for objects of SignalpResult S4 class,...

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

accessor functions for objects of SignalpResult S4 class, intermediate and final outputs of the signalp prediction step

accessors for SignalpResult objects

Usage

setMatfasta(theObject, mature_fasta)

## S4 method for signature 'SignalpResult'
setMatfasta(theObject, mature_fasta)

## S4 method for signature 'SignalpResult'
getMatfasta(theObject)

## S4 method for signature 'SignalpResult'
setSPversion(theObject, sp_version)

## S4 method for signature 'SignalpResult'
getSPversion(theObject)

## S4 method for signature 'SignalpResult'
setSPtibble(theObject, sp_tibble)

## S4 method for signature 'SignalpResult'
getSPtibble(theObject)

Arguments

theObject	SignalpResult object
mature_fasta	sequences with clipped signal peptides, AAStringSet object
sp_version	version of signalp used to generate SignalpResult object
sp_tibble	parsed signalp output in tabular format

Value

SignalpResult object

Slots

mature_fasta

fasta with mature sequences

sp_version

version of signalp used to generate this object

sp_tibble

Object of class tibble, columns:

• gene_id - unique id of the sequence

• Cmax - max raw cleavage site score (C-score)

• Cpos - amino acid position with max C-score

• Cparsed - sp2 and sp3: remove this field?

• Ymax - max combied cleavage site score (Y-score)

• Ypos - amino acid position with max Y-score

• Smax - max signal peptide score

• Spos - amino acid position with max S-score

• Smean - the average S-score of the possible signal peptide (from position 1 to the position immediately before the maximal Y-score)

• Prediction - final desision on whether the protein is secreted

Examples

# read fasta file in AAStringSet object
aa <- readAAStringSet(system.file("extdata","sample_prot_100.fasta",
package = "SecretSanta"))
# create an instance of CBSResult class
sr <- CBSResult(in_fasta = aa[1:20])
# run signalpeptide prediction and create fully populated instance of
# SignalpResult class
step1_sp2 <- signalp(sr, version = 2, organism = 'euk', run_mode = "starter",
legacy_method = 'hmm')
# access specific slots:
getOutfasta(step1_sp2)
getInfasta(step1_sp2)
getSPtibble(step1_sp2)
getSPversion(step1_sp2)
getMatfasta(step1_sp2)

gogleva/SecretSanta documentation built on May 30, 2019, 8:02 a.m.