setInfoFilter: Filter out markers based on marker quality metrics

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Filter out markers based on marker quality metrics

Description

A VCF file usually has marker quality metrics in the INFO filed and those are stored in a GDS file created via GBScleanR. This function filter out markers based on those marker quality metrics.

Usage

setInfoFilter(
  object,
  mq = 0,
  fs = Inf,
  qd = 0,
  sor = Inf,
  mqranksum = c(-Inf, Inf),
  readposranksum = c(-Inf, Inf),
  baseqranksum = c(-Inf, Inf),
  ...
)

## S4 method for signature 'GbsrGenotypeData'
setInfoFilter(object, mq, fs, qd, sor, mqranksum, readposranksum, baseqranksum)

Arguments

object	A GbsrGenotypeData object.
mq	A numeric value to specify minimum mapping quality (shown as MQ in the VCF format).
fs	A numeric value to specify maximum Phred-scaled p-value (strand bias) (shown as FS in the VCF format).
qd	A numeric value to specify minimum Variant Quality by Depth (shown as QD in the VCF format).
sor	A numeric value to specify maximum Symmetric Odds Ratio (strand bias) (shown as SOR in the VCF format).
mqranksum	A numeric values to specify the lower and upper limit of Alt vs. Ref read mapping qualities (shown as MQRankSum in the VCF format).
readposranksum	A numeric values to specify the lower and upper limit of Alt vs. Ref read position bias (shown as ReadPosRankSum in the VCF format).
baseqranksum	A numeric values to specify the lower and upper limit of Alt Vs. Ref base qualities (shown as BaseQRankSum in the VCF format).
...	Unused.

Details

Detailed explanation of each metric can be found in GATK's web site.

Value

A GbsrGenotypeData object with filters on markers.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

gds <- setInfoFilter(gds, mq = 40, qd = 20)

# Close the connection to the GDS file.
closeGDS(gds)

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.