TMhmmResult_methods: accessor functions for objects of TMhmmResult S4 class,...

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

accessor functions for objects of TMhmmResult S4 class, intermediate and final outputs of the tmhmm prediction step

Accessors for TMhmmResul objects

Usage

setTMtibble(theObject, tm_tibble)

## S4 method for signature 'TMhmmResult'
setTMtibble(theObject, tm_tibble)

## S4 method for signature 'TMhmmResult'
getTMtibble(theObject)

## S4 method for signature 'TMhmmResult'
getInMatfasta(theObject)

## S4 method for signature 'TMhmmResult'
getOutMatfasta(theObject)

Arguments

theObject	object of TMhmmREsult class
tm_tibble	parsed tmhmm output in tabular format

Value

TMhmmResult object

Slots

in_mature_fasta

input mature fasta, extracted from the input SignalpResult object

out_mature_fasta

output mature, conatins mature sequences without TM domains

tm_tibble

tibble with outputs obtained from TMHMM

• gene_id - unique id of the sequence

• length - length of the protein sequence

• ExpAA - the expected number of amino acids intransmembrane helices

• First60 - the expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein

• PredHel - the number of predicted transmembrane helices by N-best

• Topology - the topology predicted by N-best'

Examples

aa <- readAAStringSet(system.file("extdata", "sample_prot_100.fasta",
package = "SecretSanta"))
inp <- CBSResult(in_fasta = aa[1:20])
s1_sp2 <- signalp(inp, version = 2, organism = 'euk',
run_mode = "starter", legacy_method = 'hmm')
tm <- tmhmm(s1_sp2, TM = 1)
class(tm)
getTMtibble(tm)

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