CBS_methods: accessor functions for objects of 'CBSResult' S4 class,...

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

accessor functions for objects of CBSResult S4 class, minimal parent class for SecretSanat outputs

accessors for CBSResult objects

Usage

setInfasta(theObject, in_fasta)

## S4 method for signature 'CBSResult'
setInfasta(theObject, in_fasta)

## S4 method for signature 'CBSResult'
getInfasta(theObject)

## S4 method for signature 'CBSResult'
setOutfasta(theObject, out_fasta)

## S4 method for signature 'CBSResult'
getOutfasta(theObject)

## S4 method for signature 'CBSResult'
getFastas(theObject)

Arguments

theObject	CBSResult object
in_fasta	input fasta, AAStringSet object
out_fasta	output fasta, AAStringSet object

Value

CBSResult object

Slots

in_fasta

initial fasta file

out_fasta

output fasta file with only positive candidates, i.e those that passed tool filters

Examples

library(Biostrings)
# read fasta file in AAStringSet object
aa <- readAAStringSet(system.file("extdata","sample_prot_100.fasta",
                        package = "SecretSanta"))
# create an instance of CBSResult class:
cbs <- CBSResult( in_fasta = aa, out_fasta = aa)
# check that CBSResult instance is valid
validObject(cbs)

# extract in_fasta attribute
getInfasta(cbs)

# extract out_fasta attribute
getOutfasta(cbs)

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