Class GdsReader

Description

The GdsReader class provides an interface for reading GDS files.

Constructor

GdsReader(filename, ...):

filename must be the path to a GDS file or an already opened gds object.

The GdsReader constructor creates and returns a GdsReader instance pointing to this file.

Accessors

In the code snippets below, object is a GdsReader object.

getVariable(object, varname, start, count, sel=NULL, drop=TRUE): Returns the contents of the variable varname.

• start is a vector of integers indicating where to start reading values. The length of this vector must equal the number of dimensions the variable has. If not specified, reading starts at the beginning of the file (1,1,...).

• count is a vector of integers indicating the count of values to read along each dimension. The length of this vector must equal the number of dimensions the variable has. If not specified and the variable does NOT have an unlimited dimension, the entire variable is read. As a special case, the value "-1" indicates that all entries along that dimension should be read.

• sel may be specified instead of start and count. It is a list of m logical vectors, where m is the number of dimensions of varname and each logical vector should have the same size as the corresponding dimension in varname.

• drop is a logical for whether the result will be coerced to the lowest possible dimension.

The result is a vector, matrix, or array, depending on the number of dimensions in the returned values and the value of drop. Missing values (specified by a "missing.value" attribute, see put.attr.gdsn) are represented as NA. If the variable is not found in the GDS file, returns NULL.

getVariableNames(object): Returns names of variables in the GDS file.

getDimension(object, varname): Returns dimension for GDS variable varname.

getNodeDescription(object, varname): Returns description for GDS variable varname.

getAttribute(object, attname, varname): Returns the attribute attname associated with the variable varname.

hasVariable(object, varname): Returns TRUE if varname is a variable in the GDS file.

Standard Generic Methods

In the code snippets below, object is a GdsReader object.

open(object): Opens a connection to a GDS file.

close(object): Closes the connection to a GDS file.

show(object): Summarizes the contents of a GDS file.

Author(s)

Stephanie Gogarten

See Also

gdsfmt

Examples

library(SNPRelate)
gds <- GdsReader(snpgdsExampleFileName())

getVariableNames(gds)

hasVariable(gds, "genotype")
geno <- getVariable(gds, "genotype", start=c(1,1), count=c(10,10))

close(gds)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GWASTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/GdsReader-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GdsReader
> ### Title: Class GdsReader
> ### Aliases: GdsReader-class GdsReader open,GdsReader-method
> ###   close,GdsReader-method show,GdsReader-method
> ###   getDimension,GdsReader-method getNodeDescription,GdsReader-method
> ###   getVariableNames,GdsReader-method hasVariable,GdsReader-method
> ###   getVariable,GdsReader-method getAttribute,GdsReader-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> library(SNPRelate)
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
> gds <- GdsReader(snpgdsExampleFileName())
> 
> getVariableNames(gds)
 [1] "sample.id"              "snp.id"                 "snp.rs.id"             
 [4] "snp.position"           "snp.chromosome"         "snp.allele"            
 [7] "genotype"               "sample.annot/family.id" "sample.annot/father.id"
[10] "sample.annot/mother.id" "sample.annot/sex"       "sample.annot/pop.group"
> 
> hasVariable(gds, "genotype")
[1] TRUE
> geno <- getVariable(gds, "genotype", start=c(1,1), count=c(10,10))
> 
> close(gds)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>