appTEKRABber: appTEKRABber

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

appTEKRABber

Description

Provide a shiny UI for presenting the results from DE analysis and correlation analysis.

Usage

appTEKRABber(corrRef, corrCompare, DEobject)

Arguments

corrRef	correlation results for reference using corrOrtholgScale()
corrCompare	correlation results for comparison using corrOrthologScale()
DEobject	DE object using DEgeneTE()

Value

provide an interactive shinyapp

Examples

data(speciesCounts)
hmGene <- speciesCounts$hmGene
hmTE <- speciesCounts$hmTE
chimpGene <- speciesCounts$chimpGene
chimpTE <- speciesCounts$chimpTE

data(fetchDataHmChimp)
fetchData <- fetchDataHmChimp
inputBundle <- DECorrInputs(fetchData)

meta <- data.frame(
species = c(rep("human", ncol(hmGene) - 1), 
            rep("chimpanzee", ncol(chimpGene) - 1)))
            
meta$species <- factor(meta$species, levels = c("human", "chimpanzee"))
rownames(meta) <- colnames(inputBundle$geneInputDESeq2)
hmchimpDE <- DEgeneTE(
    geneTable = inputBundle$geneInputDESeq2,
    teTable = inputBundle$teInputDESeq2,
    metadata = meta,
    expDesign = TRUE)

# use only 10 rows of Genes and TEs
hmCorrResult <- corrOrthologTE(
    geneInput = hmchimpDE$geneCorrInputRef[c(1:10),],
    teInput = hmchimpDE$teCorrInputRef[c(1:10),],
    corrMethod = "pearson",
    padjMethod = "fdr")
    
chimpCorrResult <- corrOrthologTE(
    geneInput = hmchimpDE$geneCorrInputCompare[c(1:10), ],
    teInput = hmchimpDE$teCorrInputCompare[c(1:10), ],
    corrMethod = "pearson",
    padjMethod = "fdr")


#library(plotly)
#appTEKRABber(
    #corrRef = hmCorrResult,
    #corrCompare = chimpCorrResult,
    #DEobject = hmchimpDE)
    

ferygood/TEKRABber documentation built on July 31, 2024, 6:36 p.m.