Create an InformativeGenes object — create

This function runs differential expression analysis (DESeq2) and gene set enrichment analysis (GSEA) to generate a InformativeGenes object, which is necessary for creating the CASCAM object.

Usage

create_InformativeGenes(tumor_ct, tumor_lab, interested_subtype)

Arguments

tumor_ct: a data frame or matrix of the un-normalized (estimated) counts of sequencing reads or fragments from the tumor data with Rows for genes with row names of HGNC gene symbols and columns for samples.
tumor_lab: a vector of strings indicating the labels of the tumor samples.
interested_subtype: a string indicating the interested tumor subtype, and it should be included in the tumor labels.

Value

An InformativeGenes object.

References

Love, Michael I., Wolfgang Huber, and Simon Anders. "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome biology 15, no. 12 (2014): 1-21.