GDSArray-classes: GDSArray constructor and coercion methods.

In GDSArray: Representing GDS files as array-like objects

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) #> deactivate temporarily 3/4/20
GDSArray(file, "sample.annot/pop.group")

file1 <- SeqArray::seqExampleFileName("gds")
allnodes1 <- gdsnodes(file1)  ## print all available gds nodes in file1. 
allnodes1
## GDSArray(file1) #> deactivate temporarily 3/4/20
GDSArray(file1, "variant.id")
GDSArray(file1, "sample.annotation/family")
GDSArray(file1, "annotation/format/DP")
GDSArray(file1, "annotation/info/DP")
example("GDSArray")

GDSArray documentation built on April 2, 2021, 6 p.m.