import.RTEs: Loads retrotransposons counts and return a DGEList object for...

In FemeniasM/ExplorATEproject: Explore Active Transposable Elements from RNAseq data

Loads retrotransposons counts and return a DGEList object for use with edgeR.

Description

Imports count estimates and calculates an offset that corrects for changes to the average transcript length across samples (details in https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR). The function returns a DGEList for use in downstream analysis with edgeR

Usage

import.RTEs(path.sal, ref.sal, conditions, import_to = c("edgeR, DESeq2"))

Arguments

path.sal	output salmon directory
ref.sal	salmon reference build with mk.reference function
conditions	A string vector indicating the experimental conditions of each library. Example: c("S1", "S1", "S1", "S2", "S2", "S2", "S3", "S3", "S3")
import_to	A string object indicating whether to import for edgeR or DESeq2. If none is selected, transcript-level estimates are returned.

FemeniasM/ExplorATEproject documentation built on Nov. 30, 2022, 5:26 p.m.