In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

r h.i.r h.ii Gene set signature scores calculation

In order to analyze cells' expression in gene sets (signatures) level, we calculate the signature scores for each cell.

if(is.null(results$geneSets)){
    cat("* Gene sets: the default 50 hallmark gene sets from [MSigDB](http://software.broadinstitute.org/gsea/msigdb/).\n")
}else{
    cat("* Gene sets: the input gene sets list.\n")
}
if(results$geneSet.method == "average"){
    cat("* Method: relative average expression levels.")
}else if(results$geneSet.method == "GSVA"){
    cat("* Method: [GSVA](https://www.bioconductor.org/packages/release/bioc/html/GSVA.html).")
}

The calculated gene set signature scores can be found in the column GS__* of the table file cellAnnotation.txt.

Following is the heatmap for these signatures scores.

results$geneSet.plot

(Hi-res image: view)

h.ii <- h.ii + 1

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.