setSamFilter: Filter out samples

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

Filter out samples

Description

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

Usage

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

Details

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

Value

A GbsrGenotypeData object with filters on samples.

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 <- setSamFilter(gds,
                       id = getSamID(gds)[1:10],
                       missing = 0.2,
                       dp = c(5, Inf))

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

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