split_rows_with_multiple_annots: Split rows that have multiple annotations

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

Description

Rows that have X number of annotations are replicated X number of times. Multiple annotations can be due to 1) multiallelic sites which will result in an annotation for each individual allele and 2) SNPs in overlapping genes which will result in an annotation for each gene or 3) a combination of 1 and 2. The row names will be changed to have one annotation per row (that is, multiallelic SNPs are represented as biallelic sites and each snp in a gene that overlaps with another gene will be represented on a single line). The contents of the data.frame is replicated – that is, the contents of the replicated rows are NOT changed. You should run varmat_code and varmat_allele through this function separately and should expect the data.frames to have the same dimensions and same duplicated rows.

Usage

split_rows_with_multiple_annots(varmat, snp_parser_log)

Arguments

varmat	- data.frame where the rows are variants, the columns are genomes, and the row.names are annotations
snp_parser_log	- logical. TRUE when handling snp information. FALSE when handling indel information.

Value

Returns a list with the following elements (in order): 1. rows_with_multiple_annots_log - a logical vector with length of nrow(varmat_added) indicating which rows once had multiple annotations (that is, were split from one row into multiple rows) 2. rows_with_mult_var_allele_log - a logical vector with length of nrow(varmat_added) indicating which rows once had multiple annotations in the form of multiallelic sites (that is, were split from multiallelic sites to biallelic sites) 3. rows_with_overlapping_genes_log -> - a logical vector with length of nrow(varmat_added) indicating which rows once had multiple annotations in the form of overlapping genes (that is, were split from a SNP in multiple genes to each gene being represented on a single line) 4. split_rows_flag - an integer vector indicating which rows were split from from a row with multiple annotations (For example if varmat had 4 rows: 1, 2, 3, 4 with row 2 having 3 annotations and row 4 having 2 annotations, the vector would be 1 2 2 2 3 4 4). 5. varmat_added - a data.frame where the rows are variants, the columns are genomes, and the row.names are SPLIT annotations (each overlapping gene and multiallelic site represented as a single line).

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