FromFlatDF: Construct a SingleCellAssay (or derived subclass) from a...

In MAST: Model-based Analysis of Single Cell Transcriptomics

Description

SingleCellAssay are a generic container for such data and are simple wrappers around SummarizedExperiment objects. Subclasses exist that embue the container with additional attributes, eg FluidigmAssay.

Usage

FromFlatDF(
  dataframe,
  idvars,
  primerid,
  measurement,
  id = numeric(0),
  cellvars = NULL,
  featurevars = NULL,
  phenovars = NULL,
  class = "SingleCellAssay",
  check_sanity = TRUE,
  ...
)

Arguments

dataframe	A 'flattened' data.frame or data.table containing columns giving cell and feature identifiers and a measurement column
idvars	character vector naming columns that uniquely identify a cell
primerid	character vector of length 1 that names the column that identifies what feature (i.e. gene) was measured
measurement	character vector of length 1 that names the column containing the measurement
id	An identifier (eg, experiment name) for the resulting object
cellvars	Character vector naming columns containing additional cellular metadata
featurevars	Character vector naming columns containing additional feature metadata
phenovars	Character vector naming columns containing additional phenotype metadata
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.
...	additional arguments are ignored

Value

SingleCellAssay, or derived, object

Examples

data(vbeta)
colnames(vbeta)
vbeta <- computeEtFromCt(vbeta)
vbeta.fa <- FromFlatDF(vbeta, idvars=c("Subject.ID", "Chip.Number", "Well"),
primerid='Gene', measurement='Et', ncells='Number.of.Cells',
geneid="Gene",cellvars=c('Number.of.Cells', 'Population'),
phenovars=c('Stim.Condition','Time'), id='vbeta all', class='FluidigmAssay')
show(vbeta.fa)
nrow(vbeta.fa)
ncol(vbeta.fa)
head(mcols(vbeta.fa)$primerid)
table(colData(vbeta.fa)$Subject.ID)
vbeta.sub <- subset(vbeta.fa, Subject.ID=='Sub01')
show(vbeta.sub)

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