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

View source: R/gdsSubset.R

gdsSubset2R 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.

Author(s)

Adrienne Stilp


isglobal-brge/dsOmics documentation built on Nov. 11, 2024, 4:18 a.m.