SecretSanta_man: SecretSanta, main functionality

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

The SecretSanta package provides an R interface for the integrative prediction of extracellular proteins that are secreted via classical pathways.

Details

Main functionality includes:

signalp()

predict signal peptides with SignalP 2.0, SignalP 3.0 or SignalP 4.1;

tmhmm()

predict transmembrane domains with TMHMM 2.0;

topcons()

parse predictions of transmemrane domains performed by TOPCONS2;

targetp()

predict subcellular localisation with TargetP 1.1;

wolfpsort()

predict subcellular localisation with WoLF PSORT;

check_khdel()

check C-terminal ER-retention signals;

m_slicer()

generate proteins with alternative translation start sites;

ask_uniprot()

fetch known subcellular location data from UniprotKB based on uniprot ids.

S4 classes and accessor methods:

CBSResult

Basic parent S4 class with in_fasta and out_fasta slots. Accessor functions:

• getInfasta(): extract in_fasta slot;

• getOutfasta(): extract out_fasta slot;

• getFastas(): extract both/all fasta slots;

SignalpResult

S4 class, organisig outputs of signalp() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, mature_fasta, sp_tibble, sp_version. Specific accessor functions:

• getMatfasta(): extract mature_fasta slot;

• getSPtibble(): extract SignalP summary stats;

• getSPversion(): extract version of SignalP used;

TargetpResult

S4 class, organisig outputs of targetp() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, tp_tibble. Specific accessor function:

• getTPtibble(): extract parsed TargetP output in tabular format;

TMhmmResult

S4 class, organisig outputs of tmhmm() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, in_mature_fasta, out_mature_fasta, tm_tibble. Specific accessor functions:

• getInMatfasta(): extract in_mature_fasta slot;

• getOutMatfasta(): extract out_mature_fasta slot;

• getTMtibble(): extract TMHMM summary stats;

TopconsResult

S4 class, organisig outputs of topcons() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, top_tibble. Specific accessor function:

• getTOPtibble(): extract TOPCONS summary stats;

WolfResult

S4 class, organisig outputs of wolfpsort() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, wolf_tibble. Specific accessor function:

• getWOLFtibble(): extract WoLF PSORT summary;

ErResult

S4 class, organisig outputs of check_khdel() function. Inherits from CBSResult class. Slots include: in_fasta, out_fasta, retained_fasta. Specific accessor function:

• getRetainedfasta(): extract retained_fasta slot.

For detailed manual please see the vignette https://gogleva.github.io/SecretSanta/vignettes/SecretSanta-vignette.html.

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