umiAnalyzer (version 1.0.0)

filterVariants: Filter variants based on p values or depth

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)
# }
# NOT RUN {
# }