TargetpResult_methods: accessor functions for objects of TargetpResult S4 class,...

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

accessor functions for objects of TargetpResult S4 class, intermediate and final outputs of the targetp prediction step

Accessors for TargetpResult objects

Usage

setTPtibble(theObject, tp_tibble)

## S4 method for signature 'TargetpResult'
setTPtibble(theObject, tp_tibble)

## S4 method for signature 'TargetpResult'
getTPtibble(theObject)

Arguments

theObject	an object of TargetpResult class
tp_tibble	parsed targetp output in tabular format

Value

TargetpResult object

Slots

tp_tibble

tibble with outputs obtained from targetp

• gene_id - unique id of the sequence

• length - length of the protein sequence

• mTP - mitochondrial NN score

• sp - signal peptide NN score

• other - any onther NN score

• TP_localization - Prediction of localization, based on the scores; the possible values are:

• C - Chloroplast, i.e. the sequence contains cTP, a chloroplast transit peptide;

• M - Mitochondrion, i.e. the sequence contains mTP, a mitochondrial targeting peptide;

• S - Secretory pathway, i.e. the sequence contains SP, a signal peptide;

• _ - Any other location;

• "don't know" - indicates that cutoff restrictions were set (see instructions) and the winning network output score was below the requested cutoff for that category.

• RC - Reliability class, from 1 to 5, where 1 indicates the strongest prediction. RC is a measure of the size of the difference ('diff') between #' the highest (winning) and the second highest output scores. There are 5 reliability classes, defined as follows:

  • 1 - diff > 0.800;

  • 2 - 0.800 > diff > 0.600

  • 3 - 0.600 > diff > 0.400

  • 4 - 0.400 > diff > 0.200

  • 5 - 0.200 > diff

Examples

#read fasta file in AAStringSet object
aa <- readAAStringSet(system.file("extdata","sample_prot_100.fasta",
package = "SecretSanta"))
#assign this object to the input_fasta slot of SignalpResult object
inp <- CBSResult(in_fasta = aa[1:10])
tp_result <- targetp(input_obj = inp, network = 'N',
run_mode = 'starter')
class(tp_result)
getTPtibble(tp_result)
getInfasta(tp_result)
getOutfasta(tp_result)

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