DECorrInputs: Generate all the input files for TEKRABber downstream...

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

Generate all the input files for TEKRABber downstream analysis

Description

Generate all the inputs files for differentially expressed orthologous genes/TEs analysis, and for correlation analysis. The output is a list containing 6 dataframes.

Usage

DECorrInputs(fetchData)

Arguments

fetchData

output list from TEKRABber::orthologScale()

Value

create inputs for DE analysis and correlations: (1) geneInputDESeq2 (2) teInputDESeq2 (3) geneCorrInputRef (4) geneCorrInputCompare (5) TECorrInputRef (6) TECorrInputCompare

Examples

data(speciesCounts)
data(hg38_panTro6_rmsk)
hmGene <- speciesCounts$hmGene
chimpGene <- speciesCounts$chimpGene
hmTE <- speciesCounts$hmTE
chimpTE <- speciesCounts$chimpTE

## For demonstration, here we only select 1000 rows to save time
set.seed(1234)
hmGeneSample <- hmGene[sample(nrow(hmGene), 1000), ]
chimpGeneSample <- chimpGene[sample(nrow(chimpGene), 1000), ]

fetchData <- orthologScale(
    speciesRef = "hsapiens",
    speciesCompare = "ptroglodytes",
    geneCountRef = hmGeneSample,
    geneCountCompare = chimpGeneSample,
    teCountRef = hmTE,
    teCountCompare = chimpTE,
    rmsk = hg38_panTro6_rmsk
)

inputBundle <- DECorrInputs(fetchData)

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