msc.seqs: Retrieve sequences

Description Usage Arguments Value Examples

View source: R/msc.seqs.R

Description

The msc.seqs retrieves the DNA sequence of a minicircle sequence cluster (MSC) together with all its hit sequences.

Usage

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msc.seqs(fastafile, ucfile, clustnumbers, writeDNA = TRUE)

Arguments

fastafile

the name of the fasta file containing all minicircle sequences.

ucfile

the name of the uc file.

clustnumbers

a character vector containing the cluster numbers (in the format "C0", "C1", ...) of which cluster and hit sequences need to be extracted.

writeDNA

a logical parameter which is by default set to TRUE. This will write fasta files to the current directory.

Value

a table which summarizes the number of hit sequences found in the MSC, the MSC name and where the MSC is present (strain names).

one fasta file per MSC with all its hits sequences.

Examples

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data(exData)

### select a subset of MSC
Lpe <- which(exData$species == "L. peruviana")
specific <- msc.subset(matrices[[7]], subset = Lpe)

### run function
seq <- msc.seqs(fastafile = system.file("extdata", "all.minicircles.circ.fasta", package="rKOMICS"),
                ucfile = system.file("extdata", exData$ucs, package="rKOMICS")[7], 
                clustnumbers = specific$clustnumbers, writeDNA = FALSE)

rKOMICS documentation built on July 21, 2021, 5:07 p.m.