Construct a SingleCellAssay from a matrix or array of expression

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Description

If the gene expression measurements are already in a rectangular form, then this function allows an easy way to construct a SingleCellAssay object while still doing some sanity checking of inputs.

Usage

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FromMatrix(exprsArray, cData, fData, class = "SingleCellAssay")

Arguments

exprsArray

matrix or array, columns are cells, rows are genes

cData

cellData an object that can be coerced to a DataFrame, ie, data.frame, AnnotatedDataFrame. Must have as many rows as ncol(exprsArray)

fData

featureData an object that can be coerced to a DataFrame, ie, data.frame, AnnotatedDataFrame. Must have as many rows as nrow(exprsArray).

class

desired subclass of object. Default SingleCellAssay.

Value

an object of class class

Examples

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ncells <- 10
ngenes <- 5
fData <- data.frame(primerid=LETTERS[1:ngenes])
cData <- data.frame(wellKey=seq_len(ncells))
mat <- matrix(rnorm(ncells*ngenes), nrow=ngenes)
sca <- FromMatrix(mat, cData, fData)
stopifnot(inherits(sca, 'SingleCellAssay'))
stopifnot(inherits(sca, 'SummarizedExperiment0'))
##If there are mandatory keywords expected by a class, you'll have to manually set them yourself
cData$ncells <- 1
fd <- FromMatrix(mat, cData, fData)
stopifnot(inherits(fd, 'SingleCellAssay'))

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