calcIsExprs: Calculate which features are expressed in which cells using a...

Description Usage Arguments Value Examples

Description

Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.

Usage

1
calcIsExprs(object, lowerDetectionLimit = NULL, exprs_data = "counts")

Arguments

object

an SCESet object with expression and/or count data.

lowerDetectionLimit

numeric scalar giving the minimum expression level for an expression observation in a cell for it to qualify as expressed.

exprs_data

character scalar indicating whether the count data ("counts"), the transformed expression data ("exprs"), transcript-per-million ("tpm"), counts-per-million ("cpm") or FPKM ("fpkm") should be used to define if an observation is expressed or not.

Value

a logical matrix indicating whether or not a feature in a particular cell is expressed.

Examples

1
2
3
4
5
data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData=sc_example_counts)
is_exprs(example_sceset) <- calcIsExprs(example_sceset, lowerDetectionLimit = 1,
exprs_data = "exprs")


Search within the scater package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.