I came across a paper Recurrently deregulated lncRNAs in hepatocellular carcinoma in which they have done GSEA using lncRNA expression data. Check the Figure 3a and 3b, And the figure looks like below:
In the Methods section I see the following information:
We used GSEA (v2.0.13) to assess enrichment of sets of recurrently deregulated lncRNAs in other data sets. GSEA requires three input files: a gene set, expression data and phenotype labels. We used the recurrently deregulated lncRNA set (the tumorigenesis set or metastasis set) as the gene set. Expression data were derived from the TCGA cohort or published liver cancer data. For the published data, we used sample information (adjacent normal tissue, primary tumour and PVTT) as phenotype labels. Because the TCGA LIHC cohort had no PVTT or other metastasis samples, we classified primary tumour samples into invasion and non-invasion groups based on clinical information (T stages in the TNM staging system: T1 versus T2–T4). The lncRNAs were rank-ordered by differential expression (signal2Noise in GSEA v2.0.13) between the two groups.
I'm interested in making a similar figure with my data in R. Can anyone tell me how do I do that? Is there any R package to do this? Please give me an example. thanq.