In liuqivandy/scRNABatchQC: a package for quality control of multiple single cell RNAseq data

Pairwise Difference

This section identifies global pairwise difference across experiments. scRNABatchQC first detects differentially expressed genes between two experiments and then performs functional enrichment analysis on differentially expressed genes. Genes and pathways will help discriminate real biological effects from technical noise.

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plotHeatmap(as.matrix(plotData$scesMerge@metadata$diffFC$genes),"diffg")

if(hasDiffGenes){
  cat(getHeatmapCaption(as.matrix(plotData$scesMerge@metadata$diffFC$genes),"diffg"), " shows the log2 fold change of top differentially expressed genes in each pairwise comparison ")
}else{
  cat("But no differentially expressed gene detected.")
}

(logFC>r plotData$scesMerge@metadata$logFC & FDR<r plotData$scesMerge@metadata$FDR).

liuqivandy/scRNABatchQC documentation built on March 24, 2021, 11:01 p.m.