filterVariants: Filter variants based on p values or depth

In umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

Description

You can filter variants called with the the "callVariants" function based on adjusted p-value, minimum variant allele count and supply a list of assays and samples to plot.

Usage

filterVariants(
  object,
  p.adjust = 0.2,
  minVarCount = 5,
  amplicons = NULL,
  samples = NULL
)

Arguments

object	A UMIexperiment object
p.adjust	Numeric. Adjusted p value (FDR). Default is 0.2.
minVarCount	Integer. Minimum variant allele count. Default is 5.
amplicons	NULL or list of assays to plot. NULL uses all.
samples	NULL or list of samples to plot. NULL uses all.

Value

A UMIexperiment object with filtered variants. Can be used to generate VCF files.

See Also

callVariants on how to call variants.

Examples

## Not run: 
library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")

simsen <- createUmiExperiment(main)
simsen <- filterUmiObject(simsen)
simsen <- callVariants(simsen, computePrior = FALSE)
simsen <- filterVariants(simsen, p.adjust = 0.05)

## End(Not run)

umiAnalyzer documentation built on Nov. 25, 2021, 9:07 a.m.