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Multiple Sequence Alignment

Source: R/msa.R
createMSA_PDF.Rd

Generates a multiple sequence alignment from a fasta file

createMSA_PDF is a function that reads a fasta file and generates a multiple sequence alignment as a pdf

Usage

createMSA_PDF(
  fasta_path,
  out_path = NULL,
  lowerbound = NULL,
  upperbound = NULL
)

Arguments

fasta_path

Character. The path location of the fasta file to be read.

out_path

Character. The path location of the output pdf to write. Default is NULL. If value is NULL, the pdf is written to the same directory as the fasta file.

lowerbound

Numeric. The column that determines the starting location of the MSA. Default is NULL. If value is NULL, the entire multiple sequence alignment is printed.

upperbound

Numeric. The column that determines the ending location of the MSA. Default is NULL. If value is NULL, the entire multiple sequence alignment is printed.

Value

A PDF file containing the multiple sequence alignment.

Examples

if (FALSE) { # \dontrun{
createMSA_PDF(fasta_path = "path/to/your/file.fasta", 
        out_path = "path/to/output/alignment.pdf", 
        lowerbound = 10, 
        upperbound = 200)
} # }