get_indel_info_from_annotations: Grab information from each annotation

In Snitkin-Lab-Umich/snitkitr: Functions Commonly Used in the Snitkin Lab

Description

Parse annotations from row names.

Usage

get_indel_info_from_annotations(varmat)

Arguments

varmat

- data.frame where the rows are variants, the columns are genomes, and the row.names are annotations

Value

data.frame of length nrow(varmat) containing the following columns: label - string indicating "Coding SNP or Non-Coding SNP" pos - position of variant in the reference genome phage - the word NULL or the word PHAGE repeated_region - the word NULL or the word REPEAT masked - the word NULL or the word MASKED locus_tag - locus tag from gff file strand_info - returns strand information (currently incorrect until Ali fixes a bug) strand - returns + or - depending if gene is on positive or negative strand (determining this myself) ref - allele in the reference genome var - variant allele in terms of the positive strand aa_change - amino acid change in the form p.Tyr95Tyr or p.Glu75Ala variant_type - snpeff determined variant type (e.g. missense_variant, intergenic_region see snpeff manual for more info: http://snpeff.sourceforge.net/SnpEff_manual.html) snpeff_impact - snpeff determined impacted (e.g. LOW, MODERATE, MODIFIER, HIGH) nuc_pos_in_gene - variant position relative to the gene length aa_pos_in_gene - position of the codon-containing-variant relative to the gene length gene_length_in_bp - gene length in nucleotide base pairs annotation_1 - information about variant annotation_2 - information about variant ig_gene1 - if intergenic variant, first intergenic locus tag surrounding the variant ig_gene2 - if intergenic variant, second intergenic locus tag surrounding the variant intergenic - logical indicating if the variant is in an intergenic region

Snitkin-Lab-Umich/snitkitr documentation built on April 21, 2021, 10:48 a.m.