R: GDSArray constructor and coercion methods.

extract_array {GDSArray}

R Documentation

GDSArray constructor and coercion methods.

Description

extract_array: the function to extract data from a GDS file, by taking GDSArraySeed as input. This function is required by the DelayedArray for the seed contract.

GDSArray: The function to convert a gds file into the GDSArray data structure.

GDSArray example data

Usage

## S4 method for signature 'GDSArraySeed'
extract_array(x, index)

GDSArray(file, name = NA)

example(pkg = "GDSArray")

Arguments

`x`	the GDSArraySeed object
`index`	An unnamed list of subscripts as positive integer vectors, one vector per dimension in `x`. Empty and missing subscripts (represented by `integer(0)` and `NULL` list elements, respectively) are allowed. The subscripts can contain duplicated indices. They cannot contain NAs or non-positive values.
`file`	the gds file name.
`name`	the gds array node to be read into GDSArraySeed / GDSArray. For `GDSArray`, the default value for `name` is the genotype data.
`pkg`	the package name, which is "GDSArray" by default.

Value

GDSArray class object.

Examples

file <- SNPRelate::snpgdsExampleFileName()
allnodes <- gdsnodes(file)  ## print all available gds nodes in file.
allnodes
GDSArray(file)
GDSArray(file, "sample.annot/pop.group")

file1 <- SeqArray::seqExampleFileName("gds")
allnodes1 <- gdsnodes(file1)  ## print all available gds nodes in file1. 
allnodes1
GDSArray(file1)
GDSArray(file1, "variant.id")
GDSArray(file1, "sample.annotation/family")
GDSArray(file1, "annotation/format/DP/data")
GDSArray(file1, "annotation/info/DP")
example("GDSArray")

[Package GDSArray version 1.6.0 Index]