DEgeneTE: Estimate differentially expressed genes and TEs

View source: R/DEgeneTE.R

DEgeneTER Documentation

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 July 31, 2024, 6:36 p.m.