getInfo: Obtain information stored in the "annotation/info" node

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

Obtain information stored in the "annotation/info" node

Description

The "annotation/info" node stores annotation infromation of markers obtained via SNP calling tools like bcftools and GATK.

Usage

getInfo(object, var, valid = TRUE, chr = NULL, ...)

## S4 method for signature 'GbsrGenotypeData'
getInfo(object, var, valid, chr)

Arguments

object	A GbsrGenotypeData object.
var	A string to indicate which annotation info should be retrieved.
valid	A logical value. See details.
chr	A index to specify chromosome to get information.
...	Unused.

Details

If valid = TRUE, the information of the markers which are labeled TRUE in the "valid" column of the "marker" slot will be returned. If you need the number of over all markers, set valid = FALSE. validMar() tells you which markers are valid.

Value

A numeric vector of data stored in INFO node of the GDS file.

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)

# Get mapping qualities (MQ) of markers.
mq <- getInfo(gds, "MQ")

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

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