parse_indels: Parse indel variant matrix from Ali's pipeline

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

Description

Input matrices generated from internal (Ali's) variant calling pipeline. Always returns parsed annotation info. In addition, you have the option to: 1. split rows with multiple annotations (snps in overlapping genes, multiallelic snps) 2. Re-reference to the ancestral allele at that position (instead of to the reference genome) 3. Simplify the code matrix - which contains numbers from -4 to 3 indicating different information about the variants - to a binary matrix indicating simple presence/absence of a SNP at that site.

Usage

parse_indels(
  varmat_code,
  varmat_allele,
  tree = NULL,
  og = NULL,
  remove_multi_annots = FALSE,
  return_binary_matrix = TRUE,
  ref_to_anc = TRUE,
  keep_conf_only = TRUE,
  mat_suffix = "_R1_001.fastq.gz|_R1.fastq.gz|_1.fastq.gz",
  ref_to_maj = FALSE,
  parallelization = "multisession"
)

Arguments

varmat_code	- loaded data.frame or path to the varmat_code file generated from internal variant calling pipeline
varmat_allele	- loaded data.frame or path to the varmat_allele file generated from internal variant calling pipeline
tree	- optional: path to tree file or loaded in tree (class = phylo)
og	- optional: character string of the name of the outgroup (has to match what it is called in the tree)
remove_multi_annots	- logical flag indicating if you want to remove rows with multiple annotations - alternative is to split rows with mutliple annotations (default = FALSE)
return_binary_matrix	- logical flag indicating if you want to return a binary matrix (default = TRUE)
keep_conf_only	- logical flag indicating if only confident variants should be kept (1's in Ali's pipeline, otherwise 3's are also kept) (default = TRUE)
mat_suffix	Suffix to remove from code and allele matrices so the names match with the tree tip labels.
parallelization	Input to future::plan; either "multisession" (default) or "multicore" (always sets to 2 cores aka "workers")

Value

list of allele mat, code mat, binary mat and corresponding parsed annotations. output will depend on arguments to the function.

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