VariantExperiment-class {VariantExperiment} | R Documentation |
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.
VariantExperiment( assays, rowRanges = GRangesList(), colData = DelayedDataFrame(), metadata = list() ) ## S4 method for signature 'VariantExperiment' gdsfile(object) ## S4 replacement method for signature 'VariantExperiment' gdsfile(object) <- value
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 |
value |
the new gds file path for VariantExperiment object. |
VariantExperiment class and slot getters and setters.
check "?RangedSummarizedExperiment" for more details.
a VariantExperiment
object.