RRHO2

https://github.com/RRHO2/RRHO2/tree/master/vignettes/
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RRHO2 is an R package for identifying and visualizing statistically significant overlaps in gene...
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### Install RRHO2 Package

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Installs the RRHO2 package from GitHub using the devtools library. Ensure devtools is installed prior to running this command.

```r
library(devtools)
install_github("RRHO2/RRHO2")
```

--------------------------------

### Load RRHO2 Package

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Loads the RRHO2 package into the R session. This also loads the VennDiagram and futile.logger packages as dependencies.

```r
library(RRHO2)
#> Loading required package: VennDiagram
#> Loading required package: grid
#> Loading required package: futile.logger
```

--------------------------------

### Initialize RRHO2 Object

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Creates an RRHO2 object from two gene lists, specifying labels and the statistical method (e.g., 'fisher'). The 'log10.ind' argument indicates if the DDE values are log10 transformed.

```R
RRHO_obj <-  RRHO2_initialize(gene_list1, gene_list2, labels = c("list1", "list2"), log10.ind=TRUE, method = "fisher")
```

--------------------------------

### Simulate DE Data for Concordant Patterns

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Simulates gene expression data for 2000 genes to demonstrate concordant differential expression patterns. Genes 1-200 are set as up-regulated and genes 201-400 as down-regulated in both lists, with the remaining genes as noise.

```r
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;

```

--------------------------------

### Visualize RRHO2 Heatmap

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Generates a heatmap visualization of the Rank-Rank Hypergeometric Overlap results.

```R
RRHO2_heatmap(RRHO_obj)
```

--------------------------------

### Initialize RRHO2 Object

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Initializes the RRHO2 object with two gene lists and labels. Set log10.ind to TRUE if the input DDE scores are log10 transformed.

```R
RRHO_obj <-  RRHO2_initialize(gene_list1, gene_list2, labels = c("list1", "list2"), log10.ind=TRUE)
```

--------------------------------

### Simulate Gene Expression Data

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Simulates gene expression data for two lists, including p-values and direction of differential expression. This is a prerequisite for creating an RRHO2 object.

```R
set.seed(15213)
nGenes <- 2000
nDE <- 200
Genes <- paste0("Genes",1:nGenes)

list1_pvalue_1_200 <- runif(nDE,0,0.05)
list1_pvalue_201_400 <- runif(nDE,0,0.05) 
list1_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1)
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)
```

--------------------------------

### Visualize Venn Diagram for Down-Down Overlap

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Creates a Venn diagram to visualize the overlap between down-regulated genes in list1 and list2.

```R
RRHO2_vennDiagram(RRHO_obj, type="dd")
```

--------------------------------

### Visualize RRHO2 Object with Venn Diagram

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Generates a Venn diagram to visualize the overlap of differentially expressed genes. Requires an RRHO2 object and specifies the type of comparison (e.g., 'du' for down-up).

```R
RRHO2_vennDiagram(RRHO_obj, type="du")
```

--------------------------------

### Simulate Gene Expression Data for Discordant DE

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Simulates p-value data for discordant differential expression patterns between two gene lists. List1 has up-regulated then down-regulated genes, while List2 has down-regulated then up-regulated genes.

```R
set.seed(15213)
nGenes <- 2000
nDE <- 200
Genes <- paste0("Genes",1:nGenes)

list1_pvalue_1_200 <- runif(nDE,0,0.05)
list1_pvalue_201_400 <- runif(nDE,0,0.05) 
list1_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1)
list1_DDE <- c(-log10(list1_pvalue_1_200) * (-1), -log10(list1_pvalue_201_400), -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)
```

--------------------------------

### Simulate Gene Expression Data for Concordant DE

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Simulates p-value data for up-regulated, down-regulated, and non-changed genes for two gene lists. This is used to create input data frames for RRHO2.

```R
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)
```

--------------------------------

### View Head of Down-Down Overlap Gene Lists

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Displays the first few genes from the down-regulated gene lists in list1, list2, and their overlap.

```R
## down regulation genes in list1
head(RRHO_obj$genelist_dd$gene_list1_dd)

## down regulation genes in list2
head(RRHO_obj$genelist_dd$gene_list2_dd)

## overlap between down regulation genes in list1 and list2
head(RRHO_obj$genelist_dd$gene_list_overlap_dd)
```

--------------------------------

### View Head of Down-Regulation Gene Lists

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Displays the first few genes from the down-regulated gene lists within the RRHO object. Useful for inspecting the data structure.

```R
head(RRHO_obj$genelist_du$gene_list1_du)
```

```R
head(RRHO_obj$genelist_du$gene_list2_du)
```

```R
head(RRHO_obj$genelist_du$gene_list_overlap_du)
```

--------------------------------

### Extract Gene Lists for Down-Up Overlap

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Retrieves gene lists corresponding to down-regulated genes in list1 and up-regulated genes in list2, and their overlap. This is used for discordant pattern analysis.

```R
## gene lists (down regulation in list1 and up regulation in list 2) that provide the most significant overlap
RRHO_obj$genelist_du

## down regulation genes in list1
RRHO_obj$genelist_du$gene_list1_du

## down regulation genes in list2
RRHO_obj$genelist_du$gene_list2_du

## overlap between down regulation genes in list1 and list2
RRHO_obj$genelist_du$gene_list_overlap_du
```

--------------------------------

### Extract Gene Lists for Down-Down Overlap

Source: http://htmlpreview.github.io/?https://github.com/RRHO2/RRHO2/blob/master/vignettes/RRHO2.html

Retrieves gene lists corresponding to down-regulated genes in both list1 and list2, and their overlap. This is useful for identifying concordant down-regulation.

```R
## gene lists (down regulation in list1 and down regulation in list 2) that provide the most significant overlap
RRHO_obj$genelist_dd

## down regulation genes in list1
RRHO_obj$genelist_dd$gene_list1_dd

## down regulation genes in list2
RRHO_obj$genelist_dd$gene_list2_dd

## overlap between down regulation genes in list1 and list2
RRHO_obj$genelist_dd$gene_list_overlap_dd
```
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