setSubsetAssay: Method for storing new assays inside subsets in...

Description Usage Arguments Value Examples

Description

Store a new subset assay inside a specified subset in the input ExperimentSubset object.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

## S4 method for signature 
## 'SubsetRangedSummarizedExperiment,character,ANY,character'
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

## S4 method for signature 'SubsetSingleCellExperiment,character,ANY,character'
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

## S4 method for signature 'SubsetSummarizedExperiment,character,ANY,character'
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

## S4 method for signature 'SubsetSpatialExperiment,character,ANY,character'
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

## S4 method for signature 
## 'SubsetTreeSummarizedExperiment,character,ANY,character'
setSubsetAssay(x, subsetName, inputMatrix, subsetAssayName)

Arguments

x

ExperimentSubset Specify the input object.

subsetName

character(1) Specify the name of the existing subset inside which the new subset assay should be stored.

inputMatrix

dgCMatrix The input subset assay.

subsetAssayName

character(1) Specify the name of the new assay against the inputMatrix parameter.

Value

Updated ExperimentSubset object with the new assay stored inside the specified subset.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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")
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
es

campbio/ExperimentSubset documentation built on Sept. 10, 2021, 3:09 p.m.