DEgeneTE: Estimate differentially expressed genes and TEs

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

Estimate differentially expressed genes and TEs

Description

To estimate differentially expressed genes and TEs, DEgeneTE() takes gene inputs and TE inputs from the results using the DECorrInputs function. You need to specify your metadata and expDesign based on your design. If you also want to save the output, please specify the fileDir parameter.

Usage

DEgeneTE(geneTable, teTable, metadata, expDesign=TRUE, fileDir=NULL)

Arguments

geneTable	gene input table from using DECorrInputs()
teTable	TE input table from using DECorrInputs()
metadata	an one column dataframe with rownames same as the column name of gene/te count table. Column name must be species or experiment.
expDesign	Logic value for comparing between or within species. TRUE for comparing between two species, and FALSE for comparing between control and treatment.
fileDir	the name and path of directory for saving output files. Default is NULL.

Value

return DESeq2 res and normalized gene counts.

Examples

## comparing between species: 
## (1) set expDesign = TRUE 
## (2) column name of metadata needs to be "species".

data(fetchDataHmChimp)
fetchData <- fetchDataHmChimp

inputBundle <- DECorrInputs(fetchData)

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"))

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

ferygood/TEKRABber documentation built on Jan. 29, 2024, 6:34 p.m.