resetCallFilter: Set the origina; data to be used in GBScleanR's functions

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

Set the origina; data to be used in GBScleanR's functions

Description

Set the "genotype" node and the "data" node as primary nodes for genotype data and read count data. The data stored in the primary nodes are used in the functions of GBScleanR.

Usage

resetCallFilter(object, ...)

## S4 method for signature 'GbsrGenotypeData'
resetCallFilter(object)

Arguments

object	A GbsrGenotypeData object.
...	Unused.

Details

A GbsrGenotypeData object storing information of the primary node of genotype data and read count data. All of the functions implemented in GBScleanR check the primary nodes and use data stored in those nodes. setCallFilter() create new nodes storing filtered genotype calls and read counts in a GDS file and change the primary nodes to "filt.genotype" and "filt.data" for genotype and read count data, respectively. resetCallFilter() set back the nodes to the original, those are "genotype" and "data" for genotype and read count data, respectively.

Value

A GbsrGenotypeData object.

Examples

# Create a GDS file from a sample VCF file.
vcf_fn <- system.file("extdata", "sample.vcf", package = "GBScleanR")
gds_fn <- tempfile("sample", fileext = ".gds")
gbsrVCF2GDS(vcf_fn = vcf_fn, out_fn = gds_fn, force = TRUE)

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds <- loadGDS(gds_fn)

# Filter out set zero to read counts and
# missing to genotype calls of which meet the criteria.
gds <- setCallFilter(gds, dp_count = c(5, Inf))

# Now any functions of [GBScleanR] reference the genotype data
# stored in the "filt.genotype" node of the GDS file.

# If you need to set the "genotype" node, where store the raw genotype data
# as genotype to be referenced by the functions of GBScleanR,
# run the following.
gds <- resetCallFilter(gds)

# Reopening the connection to the GDS file also set the raw genotype again.
gds <- loadGDS(gds)

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

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