targetp: predict subcellular protein localization with TargetP

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

This function calls local targetp to predict subcellular localisation of a protein.

For large inputs (>1000 sequences) will automatically run as a massive paralle job.

Usage

targetp(input_obj, network = c("P", "N"), run_mode = c("starter", "piper"),
  paths = NULL, cores = NULL)

Arguments

input_obj	an instance of CBSResult class containing protein sequences in one of the slots
network	P - for plants; N - for non-plants;
run_mode	starter - if it is the first step in pipeline; piper - if you run this function on the output of other CBS tools;
paths	if targetp is not acessible globally, a file conatining a full path to it's executable should be provided; for details please check SecretSanta vignette.
cores	optional arguments, number of cores to run the parallel process on. If not set default will be 1.

Value

an object of TargetpResult class

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 CBSResult object
inp <- CBSResult(in_fasta = aa[1:10])
# run target prediction
tp_result <- targetp(input_obj = inp, network = 'N', run_mode = 'starter')

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