TENxGenomics-class: Create and manipulate a reference to 10xGenomics data.
In mtmorgan/TENxGenomics: Interface to 10x Genomics data

The TENxGenomics class provides a simple interface to subset and input 10xGenomics' 1M_neurons_filtered_gene_bc_matrices_h5.h5 file. Subsetting is a light-weight operation; input (typically of the subset matrix) is as a dense matrix and hence consumes memory.

TENxGenomics(h5path, group = "mm10")

## S4 method for signature 'TENxGenomics'
dim(x)

## S4 method for signature 'TENxGenomics'
dimnames(x)

## S4 method for signature 'TENxGenomics,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'TENxGenomics'
show(object)

## S3 method for class 'TENxGenomics'
as.matrix(x, ..., withDimnames = TRUE)

as.dgCMatrix(x, ..., withDimnames = TRUE)

`h5path`	character(1) file path to a 1M_neurons_*.h5 file.
`group`	character(1) hdf5 group (e.g., “mm10”) containing scRNA-seq data.
`x`	A `TENxGenomics-class` instance.
`i`	integer(), numeric(), character(), or logical() index into rows of `x`.
`j`	integer(), numeric(), character(), or logical() index into columns of `x`.
`...`	Additional arguments, ignored.
`drop`	logical(1) TRUE only.
`object`	A `TENxGenomics-class` instance.
`withDimnames`	logical(1) Include dimnames on returned matrix?

TENxGenomics() returns a TENxGenomics-class instance.

as.matrix(tenx) and as(tenx, "matrix") return a matrix with dim and dimnames equal to tenx, and values the read counts overlapping corresponding genes and samples. Use as.matrix(withDimnames=FALSE) to suppress dimnames on the returned matrix. NOTE: consider the size of the matrix, prod(as.numeric(dim(tenx))) before invoking this function.

as.dgCMatrix(tenx) and as(tenx, "dgCMatrix") return a sparse matrix (from the Matrix package) with dim and dimnames equal to tenx, and values the read counts overlapping corresponding genes and samples. Use as.matrix(withDimnames=FALSE) to suppress dimnames on the returned matrix.

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