CompareedgeRGLM: Creates a summary table with the number of genes under- or...

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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)

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.