tenxSummarizedExperiment: Create a 'SummarizedExperiment' from an 10xGenomics hdf5...

In mtmorgan/TENxGenomics: Interface to 10x Genomics data

Description

The SummarizedExperiment assay() contains the TENxGenomics object corresponding to the underlying hdf5 file. It also contains row and column annotations provided by the user or inferred from the hdf5 file. Inferred data requires a simple match between the file name prefix and “1M_neurons_”; if the file name prefix does not match, row and column annotations are not created.

Usage

tenxSummarizedExperiment(h5path, i, j, rowData, colData)

as.tenxSummarizedExperiment(x, rowData, colData)

matrixSummarizedExperiment(h5path, i, j, rowData, colData)

as.matrixSummarizedExperiment(x, rowData, colData)

dgCMatrixSummarizedExperiment(h5path, i, j, rowData, colData)

as.dgCMatrixSummarizedExperiment(x, rowData, colData)

Arguments

h5path	character(1) file path to a 1M_neurons_*.h5 file.
i	Optional integer(), character(), or logical() index used to subset rows (genes) of the TENxGenomics object.
j	Optional integer(), character(), or logical() index used to subset columns (samples) of the TENxGenomics object.
rowData	Optional DataFrame() with as many rows as there are genes in the 10xGenomics file or object. If missing, an object is created with 'gene' and 'genename' fields from the hdf5 file.
colData	Optional DataFrame() with as many rows as there are samples in the 10xGenomics file or object. If missing, and object is constructed from the barcodes of the hdf5 file. The sequence and library portions are separated, and the mouse is inferred (libraries <= 69 are from mouse "A", others are from mouse "B").
x	A TENxGenomics-class instance.

Value

tenxSummarizedExperiment() and as.tenxSummarizedExperiment() return a SummarizedExperiment instance where the assay() data are represented as a TENxGenomics object. Down-stream analysis will typically extract this object from (a subset of) the SummarizedExperiment, and coerce it to a, e.g,. matrix, as.matrix(assay(se[, 1:100])).

assay() and assays() must use withDimnames=FALSE when called on a tenxSummarizedExperiment-created instance; dimnames are from the underlying file rather than SummarizedExperiment.

matrixSummarizedExperiment() and as.matrixSummarizedExperiment() return a SummarizedExperiment instance where the assay() data are represented as a base::matrix object. There are practical limits to the size of this object (e.g., 20k samples); the code is most efficient when consecutive samples are selected.

dgCMatrixSummarizedExperiment() and as.dgCMatrixSummarizedExperiment() return a SummarizedExperiment instance where the assay() data are represented as a Matrix::dgCMatrix object. There are practical limits to the size of this object; the code is most efficient when consecutive samples are selected.

mtmorgan/TENxGenomics documentation built on May 23, 2019, 8:19 a.m.