makeVariantExperimentFromGDS: makeVariantExperimentFromGDS

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

makeVariantExperimentFromGDS

Description

Conversion of gds files into SummarizedExperiment object.

Usage

makeVariantExperimentFromGDS(
  file,
  ftnode,
  smpnode,
  assayNames = NULL,
  rowDataColumns = NULL,
  colDataColumns = NULL,
  rowDataOnDisk = TRUE,
  colDataOnDisk = TRUE,
  infoColumns = NULL
)

makeVariantExperimentFromSEQGDS(
  file,
  ftnode = "variant.id",
  smpnode = "sample.id",
  assayNames = NULL,
  rowDataColumns = NULL,
  colDataColumns = NULL,
  infoColumns = NULL,
  rowDataOnDisk = TRUE,
  colDataOnDisk = TRUE
)

makeVariantExperimentFromSNPGDS(
  file,
  ftnode = "snp.id",
  smpnode = "sample.id",
  assayNames = NULL,
  rowDataColumns = NULL,
  colDataColumns = NULL,
  rowDataOnDisk = TRUE,
  colDataOnDisk = TRUE
)

Arguments

file	the GDS file name to be converted.
ftnode	the node name for feature id (e.g., "variant.id", "snp.id", etc.).
smpnode	the node name for sample id (e.g., "sample.id").
assayNames	the gds node name that will be read into the assays slot and be represented as DelayedArray object.
rowDataColumns	which columns of rowData to import. The default is NULL to read in all variant annotation info.
colDataColumns	which columns of colData to import. The default is NULL to read in all sample related annotation info.
rowDataOnDisk	whether to save the rowData as DelayedArray object. The default is TRUE.
colDataOnDisk	whether to save the colData as DelayedArray object. The default is TRUE.
infoColumns	which columns of infoColumns to import for "SEQ_ARRAY" ("SeqVarGDSClass" gds class). The default is NULL to read in all available info columns.

Value

An VariantExperiment object.

Examples

## gds file from DNA-seq data

seqfile <- SeqArray::seqExampleFileName(type="gds")
ve <- makeVariantExperimentFromGDS(seqfile)
## all assay data
names(assays(ve))
showAvailable(seqfile)

## only read specific columns for feature / sample annotation. 

assayNamess <- showAvailable(seqfile)$assayNames
rowdatacols <- showAvailable(seqfile)$rowDataColumns
coldatacols <- showAvailable(seqfile)$colDataColumns
infocols <- showAvailable(seqfile)$infoColumns
ve1 <- makeVariantExperimentFromGDS(
seqfile,
assayNames = assayNamess[2],
rowDataColumns = rowdatacols[1:3],
colDataColumns = coldatacols[1],
infoColumns = infocols[c(1,3,5,7)],
rowDataOnDisk = FALSE,
colDataOnDisk = FALSE)
assay(ve1)

## the rowData(ve1) and colData(ve1) are now in DataFrame format 

rowData(ve1)
colData(ve1)

## gds file from genotyping data

snpfile <- SNPRelate::snpgdsExampleFileName()
ve <- makeVariantExperimentFromGDS(snpfile)
rowData(ve)
colData(ve)
metadata(ve)

## Only read specific columns for feature annotation.

showAvailable(snpfile)
ve1 <- makeVariantExperimentFromGDS(snpfile, rowDataColumns=c("snp.allele"))
rowRanges(ve1)

## use specific conversion functions for certain gds types

veseq <- makeVariantExperimentFromSEQGDS(seqfile)
vesnp <- makeVariantExperimentFromSNPGDS(snpfile)

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