SelectTopGenes {ILoReg} | R Documentation

## Select top or bottom N genes based on a selection criterion

### Description

The SelectTopGenes function enables selecting top or bottom N genes based on a criterion (e.g. log2FC or adj.p.value).

### Usage

    SelectTopGenes(
      gene.markers = NULL,
      top.N = 10,
      criterion.type = "log2FC",
      inverse = FALSE
    )

### Arguments

`gene.markers` | A data frame of the gene markers found by FindAllGeneMarkers function.
`top.N` | How many top or bottom genes to select. Default is `10`.
`criterion.type` | Which criterion to use for selecting the genes. Default is "log2FC".
`inverse` | Whether to select bottom instead of top N genes. Default is `FALSE`.

### Value

an object of 'data.frame' class

### Examples

    library(SingleCellExperiment)
    sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
    sce <- PrepareILoReg(sce)
    ## These settings are just to accelerate the example, use the defaults.
    sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
    sce <- RunPCA(sce,p=5)
    sce <- HierarchicalClustering(sce)
    sce <- SelectKClusters(sce,K=5)
    gene_markers <- FindAllGeneMarkers(sce)
    ## Select top 10 markers based on log2 fold-change
    top10_log2FC <- SelectTopGenes(gene_markers,
                                   top.N = 10,
                                   criterion.type = "log2FC",
                                   inverse = FALSE)

[Package ILoReg version 1.0.0 Index]