countGenotype: Count genotype calls and alleles per sample and per marker.

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

Count genotype calls and alleles per sample and per marker.

Description

This function calculates several summary statistics of genotype calls and alleles per marker and per sample. Those values will be stored in the SnpAnnotaionDataFrame slot and the sample slot and obtained via getter functions, e.g.s getCountGenoRef(), getCountAlleleRef(), and getMAF().

Usage

countGenotype(object, target = "both", node = "raw", ...)

## S4 method for signature 'GbsrGenotypeData'
countGenotype(object, target, node)

Arguments

object	A GbsrGenotypeData object.
target	Either of "marker" and "sample".
node	Either of "raw", "filt", and "cor". See details.
...	Unused.

Details

#' Genotype call data can be obtained from the "genotype" node, the "filt.genotype" node, or the "corrected.genotype" node of the GDS file with node = "raw", node = "filt", or node = "raw", respectively. The setCallFilter() function generate filtered genotype call data in the "filt.genotype" node which can be accessed as mentioned above. On the other hand, the "corrected.genotype" node can be generated via the estGeno() function.

Value

A GbsrGenotypeData object with genotype count information.

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 genotype count information and store them in the
# [marker] and [sample] slots of the [GbsrGenotypeData] object.
gds <- countGenotype(gds)

# Get the proportion of missing genotype per sample.
sample_missing_rate <- getCountGenoMissing(gds,
                                           target = "sample",
                                           prop = TRUE)

# Get the minor allele frequency per marker.
marker_minor_allele_freq <- getMAF(gds, target = "marker")

# Draw histograms of the missing rate per sample and marker.
histGBSR(gds, stats = "missing")

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

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