Get subset assay from an ExperimentSubset object.
Source: R/allGenerics.R, R/SubsetRangedSummarizedExperiment.R, R/SubsetSingleCellExperiment.R, and 3 more
getSubsetAssay.RdGet subset assay from an ExperimentSubset object.
Usage
getSubsetAssay(x, subsetName, subsetAssayName = NULL)
# S4 method for class 'SubsetRangedSummarizedExperiment'
getSubsetAssay(x, subsetName, subsetAssayName = NULL)
# S4 method for class 'SubsetSingleCellExperiment'
getSubsetAssay(x, subsetName, subsetAssayName = NULL)
# S4 method for class 'SubsetSummarizedExperiment'
getSubsetAssay(x, subsetName, subsetAssayName = NULL)
# S4 method for class 'SubsetSpatialExperiment'
getSubsetAssay(x, subsetName, subsetAssayName = NULL)
# S4 method for class 'SubsetTreeSummarizedExperiment'
getSubsetAssay(x, subsetName, subsetAssayName = NULL)Arguments
- x
Input
ExperimentSubsetobject.- subsetName
The name of the subset to fetch the assay from, or an assay seen in a subset written as
"subset/assay".- subsetAssayName
character(1)The name of an assay seen in the subsetsubsetName: one stored withsetSubsetAssay, or one linked from its parent. DefaultNULL, which returns the subset's slice of itsparentAssay.
Examples
data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es,
"subset1",
rows = c(10,11,50,56,98,99,102,105,109, 200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
getSubsetAssay(es, "subset1")
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 10 column names ‘TTAGTTCTCGTAGGAG’, ‘GGCTGGTGTCTCGTTC’, ‘TCGCGTTGTTAAGTAG’ ... ]]
#>
#> OPCML . . . . . . . . . .
#> RP11-338K17.8 . . . . . . . . . .
#> RP11-770J1.3 . . . . . . . . . .
#> NPSR1 . . . . . . . . . .
#> AC060835.1 . . . . . . . . . .
#> GABRA2 . . . . . . . . . .
#> PRDM16 . . . . . . . . . .
#> CAB39 . . . . . . . . . .
#> LYRM1 . . 1 2 . . . . . 1
#> RP1-178F10.3 . . . . . . . . . .
# store a changed copy of the subset's counts inside the subset
subset1Counts <- getSubsetAssay(es, "subset1")
es <- setSubsetAssay(es, "subset1", subset1Counts + 1, "plusOne")
getSubsetAssay(es, "subset1", subsetAssayName = "plusOne")
#> 10 x 10 Matrix of class "dgeMatrix"
#> TTAGTTCTCGTAGGAG GGCTGGTGTCTCGTTC TCGCGTTGTTAAGTAG
#> OPCML 1 1 1
#> RP11-338K17.8 1 1 1
#> RP11-770J1.3 1 1 1
#> NPSR1 1 1 1
#> AC060835.1 1 1 1
#> GABRA2 1 1 1
#> PRDM16 1 1 1
#> CAB39 1 1 1
#> LYRM1 1 1 2
#> RP1-178F10.3 1 1 1
#> GGATGTTGTAGGCATG AATCGGTTCTGATACG GTTCTCGGTATGAAAC
#> OPCML 1 1 1
#> RP11-338K17.8 1 1 1
#> RP11-770J1.3 1 1 1
#> NPSR1 1 1 1
#> AC060835.1 1 1 1
#> GABRA2 1 1 1
#> PRDM16 1 1 1
#> CAB39 1 1 1
#> LYRM1 3 1 1
#> RP1-178F10.3 1 1 1
#> TCCACACTCTTTAGTC GCGCAGTAGATGCGAC CGGACACTCAAGAAGT
#> OPCML 1 1 1
#> RP11-338K17.8 1 1 1
#> RP11-770J1.3 1 1 1
#> NPSR1 1 1 1
#> AC060835.1 1 1 1
#> GABRA2 1 1 1
#> PRDM16 1 1 1
#> CAB39 1 1 1
#> LYRM1 1 1 1
#> RP1-178F10.3 1 1 1
#> TGACTTTGTCGCGAAA
#> OPCML 1
#> RP11-338K17.8 1
#> RP11-770J1.3 1
#> NPSR1 1
#> AC060835.1 1
#> GABRA2 1
#> PRDM16 1
#> CAB39 1
#> LYRM1 2
#> RP1-178F10.3 1