gdsSubset2: Write a subset of data in a GDS file to a new GDS file
In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

gdsSubset2

R Documentation

Write a subset of data in a GDS file to a new GDS file

Description

Function addapted from GWASTools::gdsSubset. Changed the line 31 (of the source file) to have the argument allow.duplicate = TRUE

Usage

gdsSubset2(
  parent.gds,
  sub.gds,
  sample.include = NULL,
  snp.include = NULL,
  sub.storage = NULL,
  compress = "LZMA_RA",
  block.size = 5000,
  verbose = TRUE,
  allow.fork = FALSE
)

Arguments

`parent.gds`	Name of the parent GDS file
`sub.gds`	Name of the subset GDS file
`sample.include`	Vector of sampleIDs to include in sub.gds
`snp.include`	Vector of snpIDs to include in sub.gds
`sub.storage`	storage type for the subset file; defaults to original storage type
`compress`	The compression level for variables in a GDS file (see GWASTools::add.gdsn for options)
`block.size`	for GDS files stored with scan,snp dimensions, the number of SNPs to read from the parent file at a time. Ignored for snp,scan dimensions.
`verbose`	Logical value specifying whether to show progress information.
`allow.fork`	Logical value specifying whether to enable multiple forks to access the gds file simultaneously.