data(lesion_data)
data(hg38_gene_annotation)
data(hg38_chrom_size)
# Run GRIN analysis
grin.results <- grin.stats(lesion_data,
hg38_gene_annotation,
hg38_chrom_size)
# Define a list of genes (using Ensembl IDs) to include in the OncoPrint
oncoprint.genes <- c("ENSG00000148400", "ENSG00000171862", "ENSG00000171843",
"ENSG00000156531", "ENSG00000162367", "ENSG00000096968",
"ENSG00000105639", "ENSG00000118513", "ENSG00000102974",
"ENSG00000133703")
# Alternatively, select genes with multiple lesion types and significant q-values
genes.const <- grin.results$gene.hits[grin.results$gene.hits$q2.nsubj < 0.01, ]
selected.genes <- as.vector(genes.const$gene)
# Generate OncoPrint-compatible lesion matrix
oncoprint.mtx <- grin.oncoprint.mtx(grin.results, oncoprint.genes)
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