summaryVariant: Summary per variant

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Summary per variant

Description

Compute the mean, sd, min, Q1, med, mean, Q3, max of the genotype qualities per variant, also reporting the number of samples and the number of missing data.

Usage

summaryVariant(
  vcf.file,
  genome = "",
  yieldSize = NA_integer_,
  dict.file = NULL,
  seq.id = NULL,
  seq.start = NULL,
  seq.end = NULL,
  fields = "GQ",
  verbose = 1
)

Arguments

vcf.file	path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created)
genome	genome identifier (e.g. "VITVI_12x2")
yieldSize	number of records to yield each time the file is read from (see ?TabixFile) if seq.id is NULL
dict.file	path to the SAM dict file (see https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary) if seq.id is specified with no start/end
seq.id	sequence identifier to work on (e.g. "chr2")
seq.start	start of the sequence to work on
seq.end	end of the sequence to work on
fields	genotype field(s) of the VCF to parse ("DP"/"GQ"/c("DP","GQ"))
verbose	verbosity level (0/1)

Value

list of matrices (one per field) with one row per variant and 9 columns (n, na, mean, sd, min, q1, med, q3, max)

Author(s)

Timothee Flutre

See Also

varqual2summary

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.