aucellResults-class: Wrapper to the matrix that stores the AUC or the cell...

In AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Description

This class extends SummarizedExperiment to contain the AUC matrix and cell rankings (as 'assays').

The results are stored in the assays slot, but they can be accessed through the regular methods (i.e. nrow, rownames... )

Types:

- "AUC": The assays contains the AUC for the gene-sets (or region-sets) & cells.

- "ranking": The assays contains the gene rankings for each cell.

Usage

## S4 method for signature 'aucellResults'
show(object)

getAUC(object)

## S4 method for signature 'aucellResults'
getAUC(object)

getRanking(object)

## S4 method for signature 'aucellResults'
getRanking(object)

## S4 method for signature 'aucellResults'
cbind(..., deparse.level = 1)

## S4 method for signature 'aucellResults'
rbind(..., deparse.level = 1)

Arguments

object	Results from AUCell_buildRanking
...	(Only for cbind) or AUCell_calcAUC.
deparse.level	(Only for cbind)

Value

• show: Prints a summary of the object

• getAUC: Returns the matrix containing the AUC

• getRanking: Returns the matrix containing the rankings

• cbind: Combines objects by columns (cbind on assays); other other slots are conserved from the first object provided as argument. Both, ranking and AUC are calculated by column (cell or sample). Therefore, it is fine to merge objects as long as they come from equivalent datasets (and keep same genes/genesets, etc...)

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.


############# Fake run of AUCell #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)

# Running AUCell
cells_rankings <- AUCell_buildRankings(exprMatrix)
fewGenes <- sample(rownames(exprMatrix), 10)
otherGenes <- sample(rownames(exprMatrix), 5)
geneSets <- list(geneSet1=fewGenes,
                 geneSet2=otherGenes)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1)
##############################################

#Exploring the output:
cells_AUC

class(cells_AUC)

# Extracting the AUC matrix:
getAUC(cells_AUC)[,1:5]

# Subsetting and regular manipulation methods are also available:
cells_AUC[1:2,]
cells_AUC[,3:4]

dim(cells_AUC)
nrow(cells_AUC)
ncol(cells_AUC)
colnames(cells_AUC)
rownames(cells_AUC)

### Merging 2 objects (ranking or AUC):
sample1 <- cells_AUC[,10:20]
sample2 <- cells_AUC[,100:140]
cbind(sample1, sample2)

AUCell documentation built on Nov. 8, 2020, 5:51 p.m.