FieldEffectCrc: Tumor, tumor-adjacent normal, and healthy colorectal...

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

Description

Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 hosted on Synapse:

<https://www.synapse.org/#!Synapse:syn22237139/files/>

Data have been parsed into three SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

Details

Includes data as well as two simple helper functions to execute common manipulations of the data:

• make_txi: makes a tximport-style list from a SummarizedExperiment object for downstream use

• reorder_assays: reorders the assays of a SummarizedExperiment object so that counts is the first assay

See the package vignette for examples of using these data in differential gene expression analysis.

browseVignettes("FieldEffectCrc")

Details of how the SummarizedExperiment objects were created from count matrices are available in the inst/scripts/ directory of the source package in the make-data.R file.

Author(s)

Chris Dampier

Examples

  ## load ExperimentHub package
  library(ExperimentHub)

  ## load hub
  hub <- ExperimentHub::ExperimentHub()

  ## list resources associated with package
  x <- ExperimentHub::listResources(hub, "FieldEffectCrc")
  x

  ## query hub for package resources
  r <- AnnotationHub::query(hub, c("FieldEffectCrc"))
  r

  ## download selected resource by position
  ## output is SummarizedExperiment
  ## cohort C is smaller than cohort A and quicker to load
  data <- r[[3]]
  data

  ## download selected resource by hub id
  ## output is SummarizedExperiment
  data <- r[["EH3526"]]
  data

  ## download selected resource by filter
  ## output is list of SummarizedExperiments
  data <- ExperimentHub::loadResources(hub, "FieldEffectCrc", "cohort C")
  data

  ## make a txi object
  se <- r[["EH3526"]]
  txi <- make_txi(se)
  str(txi)

  ## move counts to the first assay slot
  se <- r[["EH3526"]]
  se <- reorder_assays(se)
  se

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