appTEKRABber: Visualize TEKRABber results with shiny app

In ferygood/TEKRABber: An R package estimates the correlations of orthologs and transposable elements between two species

Visualize TEKRABber results with shiny app

Description

To help user explore their results using TEKRABber, this function visualizes the results using a self-written shiny app with two tabs, including the expression and correlation of genes and TEs. To run it, you need to create four variables and assign them with your DE result, correlation results and metadata to appDE, appRef, appCompare and appMeta. Please see the example below for more details.

Usage

appTEKRABber()

Value

An app to display differentially expressed genes/TEs and the correlation results

Examples

data(fetchDataHmChimp)
fetchData <- fetchDataHmChimp

inputBundle <- DECorrInputs(fetchData)

# create metadata for DE analysis
meta <- data.frame(species=c(rep("human", ncol(fetchData$geneRef) - 1), 
    rep("chimpanzee", ncol(fetchData$geneCompare) - 1))
)
rownames(meta) <- colnames(inputBundle$geneInputDESeq2)
meta$species <- factor(meta$species, levels = c("human", "chimpanzee"))

# DE analysis
hmchimpDE <- DEgeneTE(
    geneTable = inputBundle$geneInputDESeq2,
    teTable = inputBundle$teInputDESeq2,
    metadata = meta,
    expDesign = TRUE
)

data(speciesCorr)
hmGeneCorrInput <- assay_tekcorrset(speciesCorr, "gene", "human")
hmTECorrInput <- assay_tekcorrset(speciesCorr, "te", "human")
chimpGeneCorrInput <- assay_tekcorrset(speciesCorr, "gene", "chimpanzee")
chimpTECorrInput <- assay_tekcorrset(speciesCorr, "te", "chimpanzee")

# Correlation analysis
hmCorrResult <- corrOrthologTE(
    geneInput = hmGeneCorrInput,
    teInput = hmTECorrInput,
    corrMethod = "pearson",
    padjMethod = "fdr"
)
chimpCorrResult <- corrOrthologTE(
    geneInput = chimpGeneCorrInput,
    teInput = chimpTECorrInput,
    corrMethod = "pearson",
    padjMethod = "fdr"
)

# assign results and metadata to appDE, appRef, appCompare, and appMeta
appDE <- hmchimpDE
appRef <- hmCorrResult
appCompare <- chimpCorrResult
appMeta <- meta

if (interactive()){
    
    appTEKRABber()

}

ferygood/TEKRABber documentation built on March 11, 2023, 5:03 a.m.