FromMatrix {MAST} | R Documentation |
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.
FromMatrix(exprsArray, cData, fData, class = "SingleCellAssay", check_logged = TRUE)
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 |
fData |
featureData an object that can be coerced to a DataFrame, ie, data.frame, AnnotatedDataFrame. Must have as many rows as |
class |
desired subclass of object. Default |
check_logged |
(default: |
an object of class class
defaultAssay
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'))