effectR (version 1.0.2)

effector.summary: Returns non-redundant sequences from hmm.search or regex.search and generates a motif table

Description

This function summarize the results from regex.search or hmm.search.

Usage

effector.summary(hmm.result, motif = "RxLR", reg.pat = NULL)

Arguments

hmm.result

A list of SeqFastadna objects obtained from regex.search or hmm.search

motif

A character string indicating the motif of interest. Motifs for two cytoplasmic effectors are added to the function: RxLR or CRN effectors. Each of these motifs are associated with a by-default REGEX (reg.pat). A third option, custom, allows for the search of custom motifs. The custom option requires the specification of the motif REGEX pattern in the reg.pat option, in a regex format. Default is RxLR

reg.pat

A character string indicating the REGEX pattern for the custom motif. The specification of the REGEX pattern in must be in regex format. Required for custom option of motif

Value

A list of two objects: Summary motif table and non-redundant sequences (only with results of hmm.search)

Examples

# NOT RUN {
fasta.file <- system.file("extdata", "test_infestans.fasta", package = "effectR")
ORF <- seqinr::read.fasta(fasta.file)
REGEX <- regex.search(ORF, motif='RxLR')
candidate.rxlr <- hmm.search(original.seq = fasta.file, regex.seq=REGEX, num.threads = 2)
effector.summary(candidate.rxlr)
# Custom motifs
reg.pat <- "^\\w{50,60}[w,v]"
REGEX <- regex.search(sequence = ORF, motif = "custom", reg.pat = reg.pat)
candidate.custom <- hmm.search(original.seq = fasta.file, regex.seq = REGEX)
effector.summary(candidate.custom, motif = "custom", reg.pat = reg.pat)

# }