check_khdel: check C-terminal ER-retention signals

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

This function checks the presence of terminal KDEL/HDEL motifs in the provided amino acid equences.

Usage

check_khdel(input_obj, pattern = c("prosite", "elm", "strict"))

Arguments

input_obj	input object of CBSResult class
pattern	ER-pattern to check for: pattern = 'prosite' - "[KRHQSA][DENQ]EL$>" pattern = 'elm' - "[KRHQSAP][DENQT]EL$" pattern = 'strict' - "[KH]DEL$"

Value

ErResult object

Examples

# check ER retention signals in CBSResult object
# before running signalp or any other
# predictions:
aa <- readAAStringSet(system.file("extdata", "sample_prot_100.fasta",
                                    package = "SecretSanta"))
inp <- CBSResult(in_fasta = aa[1:10])
# generate signalp predictions:
step1_sp2 <- signalp(inp, version = 4, organism = 'euk', 
    run_mode = 'starter')
# check ER retention signal in the signalp output, PROSITE pattern
et_result <- check_khdel(step1_sp2, pattern = 'prosite')

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