make_txi: Make a 'tximport'-style list object from a...

In BarcUVa-Seq/FieldEffectCrc: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

Description

Simple helper function to make a tximport-style txi list object for downstream use, especially with DESeq2 and the DESeqDataSetFromTximport() function.

Usage

  make_txi(
    se
  )

Arguments

se	A SummarizedExperiment object with three assays as would be downloaded from the FieldEffectCrc package.

Details

Meant to facilitate differential expression using DESeq2 as explained in the FieldEffectCrc package vignette.

browseVignettes("FieldEffectCrc")

Value

A list object with 4 elements, including 3 matrices and a character string. The matrices are in the following order: abundance, counts, length. The character string specifies whether tximport has scaled the counts. None of the counts have been scaled in the FieldEffectCrc package.

Author(s)

Chris Dampier

Examples

  ## make a txi object
  hub <- ExperimentHub::ExperimentHub()
  r <- AnnotationHub::query(hub, c("FieldEffectCrc"))
  se <- r[["EH3526"]]
  txi <- make_txi(se)
  str(txi)
  dds <- DESeq2::DESeqDataSetFromTximport(
            txi,
            SummarizedExperiment::colData(se),
            ~ sampType
          )

BarcUVa-Seq/FieldEffectCrc documentation built on Sept. 23, 2020, 2:53 a.m.