screening: Screen for a set of genes of interst (e.g. virulence genes)...

In JeromeAmbroise/Pathogenomics:

Description

screening returns a vector indicating if the genome matches each gene of interst.

Usage

screening(genomePath, genesPath, lengthconf, identconf, outputdir)

Arguments

genomePath	A string of character corresponding to the path of the FASTA file of the genome to be screened.
genesPath	A vector of string of character corresponding to the paths of the FASTA files of the genes of interst (e.g. virulence genes).
lengthconf	The minimum accepted length of the hit (in percentage of the gene of interest).
identconf	The minimum accepted identity of the hit (in percentage of identity).
outputdir	The directory where output files are stored.

Value

result is a vector containing 0 and 1. This vector has the length of the number of genes of interest. The name of the elements of this vector corresponds to the name of the gene of interest.

Examples

genomePath <- list.files(system.file("extdata/genome", package = "Pathogenomics"),full.names=T)
Ngenomes <- length(genomePath)
genesPath <- list.files(system.file("extdata/virulence/Escherichia-coli/Virulencefinder", package = "Pathogenomics"),full.names=T)
Ngenes <- length(genesPath)
screening(genomePath= genomePath[1],genesPath=genesPath,lengthconf = 60,identconf = 90,outputdir = '7-virulence-Irenge')

JeromeAmbroise/Pathogenomics documentation built on July 19, 2019, 1:45 a.m.