FromMatrix {MAST}R Documentation

Construct a SingleCellAssay from a matrix or array of expression

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

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

Arguments

exprsArray

matrix, or a list of matrices, or an 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.

check_logged

(default: TRUE) Set FALSE to override sanity checks that try to ensure that the default assay is logged transformed. See defaultAssay for details on the "default assay" which is assumed to contain log transformed data.

Value

an object of class class

See Also

defaultAssay

Examples

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, 'SummarizedExperiment'))
##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'))

[Package MAST version 1.6.1 Index]