Implementation of improved RRHO2, for which all regions in RRHO plots are meaningful.
First you need R devtools
package installed.
- In R console
library(devtools)
install_github("RRHO2/RRHO2", build_opts = c("--no-resave-data", "--no-manual"))
-
Cahill, K. M., Huo, Z., Tseng, G. C., Logan, R. W., & Seney, M. L. (2018). Improved identification of concordant and discordant gene expression signatures using an updated rank-rank hypergeometric overlap approach. Scientific reports, 8(1), 1-11.
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Plaisier, S. B., Taschereau, R., Wong, J. A., & Graeber, T. G. (2010). Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic acids research, 38(17), e169-e169.
- Start the package
library(RRHO2)
-
Input data format
- The input gene list should have 2 columns, 1st column is the gene symbol, 2nd column is the input score.
- The score should be calculated as -log10(pvalue) * sign(effectSize)
- NA is not allowed
- Gene symbols of the two gene lists should be identical, but don't have to be in the same order
-
Simulate data
set.seed(15213)
nGenes <- 2000
nDE <- 200
Genes <- paste0("Genes",1:nGenes)
## For up-regulated genes, the input score should be calculated using-log10(pvalue) * 1;
## For down-regulated genes, the input score should be calculated using-log10(pvalue) * (-1);
list1_pvalue_1_200 <- runif(nDE,0,0.05) ## up-regulated genes
list1_pvalue_201_400 <- runif(nDE,0,0.05) ## down-regulated genes
list1_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1) ## non-changed genes
list1_DDE <- c(-log10(list1_pvalue_1_200),
-log10(list1_pvalue_201_400) * (-1),
-log10(list1_pvalue_401_2000) * sample(c(1,-1), length(list1_pvalue_401_2000), replace = TRUE))
gene_list1 <- data.frame(Genes=Genes,DDE = list1_DDE, stringsAsFactors = FALSE)
list2_pvalue_1_200 <- runif(nDE,0,0.05)
list2_pvalue_201_400 <- runif(nDE,0,0.05)
list2_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1)
list2_DDE <- c(-log10(list2_pvalue_1_200), -log10(list2_pvalue_201_400) * (-1),
-log10(list2_pvalue_401_2000) * sample(c(1,-1), length(list2_pvalue_401_2000), replace = TRUE))
gene_list2 <- data.frame(Genes=Genes,DDE = list2_DDE, stringsAsFactors = FALSE)
- Create the RRHO2 object
RRHO_obj <- RRHO2_initialize(gene_list1, gene_list2, labels = c("list1", "list2"), log10.ind=TRUE)
- Visualize the heatmap
RRHO2_heatmap(RRHO_obj)
- Visualize the Venn Diagram
RRHO2_vennDiagram(RRHO_obj, type="dd")