CSESA {CSESA}

CSESA (CRISPR-based Salmonella enterica Serotype Analyzer).

Description

The main function in CSESA package.

Usage

CSESA(in.file1 = NULL, in.file2 = NULL, out.file = NULL,
  method = c("PCR", "WGS"))

Arguments

in.file1

The first input file, the default value is NULL.

in.file2

The second input file (optional), the default value is NULL.

out.file

Into which results will be saved if this value is set. Otherwise results will be displayed on the screen.

method

The method to handle the input file(s), which can be set as "PCR" or "WGS". Choose "PCR" if the CRISPR sequence(s) from PCR amplification is entered, and choose "WGS" when entering the whole genome assembly of a Salmonella isolate.

Note

If you use the "WGS" method, please make sure you have installed the BLAST software and included it within the working path.

Examples

  CSESA(system.file("extdata", "sequence_CRIPSR1.fasta", package = "CSESA"), 
  system.file("extdata", "sequence_CRIPSR2.fasta", package = "CSESA"), method = "PCR")
  CSESA(system.file("extdata", "sequence_CRIPSR1.fasta", package = "CSESA"), method = "PCR")
  CSESA(system.file("extdata", "Salmonella_whole_genome_assembly.fasta", 
  package = "CSESA"), method = "WGS")