TopconsResult_methods: accessor functions for objects of TopconsResult S4 class

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

accessor functions for objects of TopconsResult S4 class

Accessors for TopconsResult objects

Usage

setTOPtibble(theObject, top_tibble)

## S4 method for signature 'TopconsResult'
setTOPtibble(theObject, top_tibble)

## S4 method for signature 'TopconsResult'
getTOPtibble(theObject)

Arguments

theObject	an object of TopconsResult class
top_tibble	parsed TOPCONS output in tabular format

Value

TopconsResult object

Slots

top_tibble

tibble with outputs obtained from topcons

• seq - intermediate sequence id

• length - length of the protein sequence

• TM - number of transmembrane domains predicted

• SP - logical, True if signal peptide is predicted, False - otherwise

• source - run type: new or cached

• run_time - run time in seconds

• gene_id - cropped sequence id (any description if present - removed) #'

Examples

aa <- readAAStringSet(system.file("extdata", "sample_prot_100.fasta",
           package = "SecretSanta"), use.names = TRUE)
inp <- CBSResult(in_fasta = aa)
# predict signal peptides:
sp <- signalp(inp, version = 2, organism = 'euk', run_mode = "starter",
legacy_method = 'hmm')
# integrate topcons predictions
p_dir <- system.file("extdata", "rst_SVw4hG.zip", package = "SecretSanta")
tpc <- topcons(input_obj = sp, parse_dir = p_dir, topcons_mode = "WEB-server",
              TM = 0, SP = TRUE)
tpc
# extract out_fasta slot
getOutfasta(tpc)
# extract topcons summary
getTOPtibble(tpc)            

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