CompareedgeRGLM {ChromSCape} | R Documentation

## Creates a summary table with the number of genes under- or overexpressed in each group and outputs several graphical representations

### Description

Creates a summary table with the number of genes under- or overexpressed in each group and outputs several graphical representations

### Usage

    CompareedgeRGLM(
      dataMat = NULL,
      annot = NULL,
      ref_group = NULL,
      groups = NULL,
      featureTab = NULL,
      norm_method = "TMMwsp"
    )

### Arguments

`dataMat` | reads matrix
`annot` | selected annotation of interest
`ref_group` | List containing one or more vectors of reference samples. Name of the vectors will be used in the results table. The length of this list should be 1 or the same length as the groups list
`groups` | List containing the IDs of groups to be compared with the reference samples. Names of the vectors will be used in the results table
`featureTab` | Feature annotations to be added to the results table
`norm_method` | Which method to use for normalizing ('upperquantile')

### Value

A dataframe containing the foldchange and p.value of each feature

### Author(s)

Eric Letouze & Celine Vallot

### Examples

    data("scExp")
    scExp_cf = correlation_and_hierarchical_clust_scExp(scExp)
    scExp_cf = choose_cluster_scExp(scExp_cf,nclust=2,consensus=FALSE)
    featureTab = as.data.frame(SummarizedExperiment::rowRanges(scExp_cf))
    rownames(featureTab) = featureTab$ID
    ref_group = list("C1"=scExp_cf$cell_id[which(scExp_cf$cell_cluster=="C1")])
    groups = list("C2"=scExp_cf$cell_id[which(scExp_cf$cell_cluster=="C2")])
    myres = CompareedgeRGLM(as.matrix(SingleCellExperiment::counts(scExp_cf)),
    annot=as.data.frame(SingleCellExperiment::colData(scExp_cf)),
       ref_group=ref_group,groups=groups, featureTab=featureTab)

[Package ChromSCape version 1.2.62 Index]