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

In campbio/ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects

Description

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

Usage

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

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.