Pre-bundled alignments — alignment

This function returns either a data frame of the pre-bundled alignments if parameter gene is missing (default behaviour), or the file name of the alignment of a supplied gene name.

Usage

alignment_file(gene)

Arguments

gene: The gene name of one of the pre-bundled alignments. Run alignment_file() to list all genes available.

Value

Either a data frame of the pre-bundled alignments if parameter gene

is missing (default behaviour), or the file name of the alignment of a supplied gene name.

Examples

# List pre-bundled alignment file names and associated genes
alignment_file()
#> # A tibble: 12 × 2
#>    gene  file                      
#>    <chr> <chr>                     
#>  1 ATM   ATM4_Spur.fasta           
#>  2 BRCA1 BRCA1_Align_Pufferfish.txt
#>  3 BRCA2 BRCA2_Puff.fasta          
#>  4 CHEK2 CHEK2_June_2010.fasta     
#>  5 MRE11 MRE11_all.fa              
#>  6 MSH6  MSH6_Align_2010a.fa       
#>  7 NBN   NBN_all.fa                
#>  8 PALB2 PALB2.fa                  
#>  9 PMS2  PMS2_Align_2010a.fa       
#> 10 RAD50 RAD50_all.fa              
#> 11 RAD51 RAD51.fa                  
#> 12 XRCC2 XRCC2_Tadh.fa             

# Retrieve the file name of an alignment
alignment_file("BRCA1")
#> [1] "BRCA1_Align_Pufferfish.txt"

# You may get the full path to an alignment file with `system.file()`
system.file("extdata", alignment_file("BRCA1"), package = "agvgd")
#> [1] "/home/runner/work/_temp/Library/agvgd/extdata/BRCA1_Align_Pufferfish.txt"