extract_fa: Retrieve descriptors from fasta file
In mmaitenat/ideafix: ideafix, DEAmination FIXing

extract_fa retrieves from fasta_filename a set of descriptors for the C:G > T:A variants defined in mutation_ids. These descriptors are relevant to their classification into deaminations or non-deaminations.

1	extract_fa(mutation_ids, fasta_filename, k = 2)

`mutation_ids`	character vector containing the ids of the loci to get the descriptors of. Id format is CHR:POS.
`fasta_filename`	character string naming the path to the reference genome FASTA file the sequencing data was aligned to.
`k`	integer with the number of bases to the right and to the left of the loci to get the genomic sequence from.

Tibble containing a set of descriptors related to the genomic base sequence ranging from locus - k to locus + k for each locus in mutation_ids. These descriptors, divided in columns, are: base two positions before, base one position before, base two positions after, base one position after, dinucleotide before and dinucleotide after.

mmaitenat/ideafix documentation built on Sept. 18, 2021, 7:55 a.m.