showAvailable: ShowAvailable

In Bioconductor/VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

ShowAvailable

Description

The function to show the available entries for the arguments within makeVariantExperimentFromGDS

Usage

showAvailable(
  file,
  args = c("assayNames", "rowDataColumns", "colDataColumns", "infoColumns"),
  ftnode,
  smpnode
)

Arguments

file	the path to the gds.class file.
args	the arguments in makeVariantExperimentFromGDS.
ftnode	the node name for feature id (e.g., "variant.id", "snp.id", etc.). Must be provided if the file format is not SNP_ARRAY or SEQ_ARRAY.
smpnode	the node name for sample id (e.g., "sample.id"). Must be provided if the file format is not SNP_ARRAY or SEQ_ARRAY.

Examples

## snp gds file
gds <- SNPRelate::snpgdsExampleFileName()
showAvailable(gds)

## sequencing gds file
gds <- SeqArray::seqExampleFileName("gds")
showAvailable(gds)

Bioconductor/VariantExperiment documentation built on Nov. 3, 2024, 8:11 a.m.