gdsSubset2: Write a subset of data in a GDS file to a new GDS file

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

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.

Author(s)

Adrienne Stilp

isglobal-brge/dsOmics documentation built on March 22, 2023, 4:01 a.m.