FromMatrix: Construct a SingleCellAssay from a matrix or array of...

In MAST: Model-based Analysis of Single Cell Transcriptomics

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_sanity = TRUE,
  check_logged = check_sanity
)

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_sanity	(default: TRUE) Set FALSE to override sanity checks that try to ensure that the default assay is log-transformed and has at least one exact zero. See defaultAssay for details on the "default assay" which is assumed to contain log transformed data.
check_logged	alias for check_sanity

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'))

Example output

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'MAST'

The following object is masked from 'package:stats':

    filter

No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
Warning message:
system call failed: Cannot allocate memory 

MAST documentation built on Nov. 8, 2020, 8:19 p.m.