setMarFilter: Filter out markers

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

Filter out markers

Description

Search markers which do not meet the criteria and label them as "invalid".

Usage

setMarFilter(
  object,
  id = NA_integer_,
  missing = 1,
  het = c(0, 1),
  mac = 0,
  maf = 0,
  ad_ref = c(0, Inf),
  ad_alt = c(0, Inf),
  dp = c(0, Inf),
  mean_ref = c(0, Inf),
  mean_alt = c(0, Inf),
  sd_ref = Inf,
  sd_alt = Inf,
  ...
)

## S4 method for signature 'GbsrGenotypeData'
setMarFilter(
  object,
  id,
  missing,
  het,
  mac,
  maf,
  ad_ref,
  ad_alt,
  dp,
  mean_ref,
  mean_alt,
  sd_ref,
  sd_alt
)

Arguments

object	A GbsrGenotypeData object.
id	A vector of integers matching with snp ID which can be retrieve by getMarID(). The markers with the specified IDs will be filtered out.
missing	A numeric value [0-1] to specify the maximum missing genotype call rate per marker
het	A numeric vector with length two [0-1] to specify the minimum and maximum heterozygous genotype call rate per marker
mac	A integer value to specify the minimum minor allele count per marker
maf	A numeric value to specify the minimum minor allele frequency per marker.
ad_ref	A numeric vector with length two specifying lower and upper limit of reference read counts per marker.
ad_alt	A numeric vector with length two specifying lower and upper limit of alternative read counts per marker.
dp	A numeric vector with length two specifying lower and upper limit of total read counts per marker.
mean_ref	A numeric vector with length two specifying lower and upper limit of mean of reference read counts per marker.
mean_alt	A numeric vector with length two specifying lower and upper limit of mean of alternative read counts per marker.
sd_ref	A numeric value specifying the upper limit of standard deviation of reference read counts per marker.
sd_alt	A numeric value specifying the upper limit of standard deviation of alternative read counts per marker.
...	Unused.

Details

For mean_ref, mean_alt, sd_ref, and sd_alt, this function calculate mean and standard deviation of reads obtained for samples at each SNP marker. If a mean read counts of a marker was smaller than the specified lower limit or larger than the upper limit, this function labels the marker as "invalid". In the case of sd_ref and sd_alt, standard deviations of read counts of each marker are checked and the markers having a larger standard deviation will be labeled as "invalid". To check valid and invalid markers, run validMar().

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)

# Summarize the information needed for filtering.
gds <- countGenotype(gds)
gds <- countRead(gds)

gds <- setMarFilter(gds,
                      id = getMarID(gds)[1:100],
                      missing = 0.2,
                      dp = c(5, Inf))

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

tomoyukif/GBScleanR documentation built on April 27, 2024, 9:06 a.m.