VariantExperiment-class: VariantExperiment-class

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

VariantExperiment-class

Description

VariantExperiment could represent big genomic data in RangedSummarizedExperiment object, with on-disk GDS back-end data. The assays are represented by DelayedArray objects; rowData and colData could be represented by DelayedDataFrame or DataFrame objects.

Usage

VariantExperiment(
  assays,
  rowRanges = GRangesList(),
  colData = DelayedDataFrame(),
  metadata = list()
)

## S4 method for signature 'VariantExperiment'
gdsfile(object)

Arguments

assays	A ‘list’ or ‘SimpleList’ of matrix-like elements, or a matrix-like object. All elements of the list must have the same dimensions, and dimension names (if present) must be consistent across elements and with the row names of ‘rowRanges’ and ‘colData’.
rowRanges	A GRanges or GRangesList object describing the ranges of interest. Names, if present, become the row names of the SummarizedExperiment object. The length of the GRanges or GRangesList must equal the number of rows of the matrices in ‘assays’.
colData	An optional DataFrame describing the samples. Row names, if present, become the column names of the VariantExperiment.
metadata	An optional ‘list’ of arbitrary content describing the overall experiment.
object	a VariantExperiment object.

Details

VariantExperiment class and slot getters and setters.

check "?RangedSummarizedExperiment" for more details.

Value

a VariantExperiment object.

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