VariantExperiment-class {VariantExperiment}R Documentation

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)

## S4 replacement method for signature 'VariantExperiment'
gdsfile(object) <- value

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.

value

the new gds file path for VariantExperiment object.

Details

VariantExperiment class and slot getters and setters.

check "?RangedSummarizedExperiment" for more details.

Value

a VariantExperiment object.


[Package VariantExperiment version 1.8.0 Index]