read_alignment {agvgd}

Read a protein sequence multiple alignment

Description

Reads a protein sequence multiple alignment (PSMA) from either a set of pre-bundled alignments, by gene name, or from a Multi-FASTA file.

Usage

read_alignment(
  gene = c("ATM", "BRCA1", "BRCA2", "CHEK2", "MRE11", "MSH6", "NBN", "PALB2", "PMS2",
    "RAD50", "RAD51", "XRCC2"),
  file = NULL
)

Arguments

gene

The gene name for which an alignment is provided with this package. Use the function alignment_file() to list the pre-bundled alignments.

file

The path to a Multi-FASTA file. If this argument is given, it takes precedence over the gene parameter.

Value

An alignment object; essentially, a character matrix, whose elements are protein residues in one-letter notation. Rows are sequences and columns are alignment positions.

Examples

# Read in the alignment for the gene XRCC2
read_alignment('XRCC2')

# Also read in the alignment for the gene XRCC2, but now by specifying
# directly the path to the file.
path <- system.file("extdata", alignment_file("XRCC2"), package = "agvgd")
read_alignment(file = path)