Build an ExploratorySummarisedExperimentList from a YAML description

Building ExploratorySummarisedExperimentList objects can be a bit fiddly. This function makes automates object construction based on a descriptor in yaml format.

Usage

eselist_from_yaml(configfile)

Arguments

configfile

A YAML-format config file describing the data to be compiled into an ExploratorySummarizedExperimentList object

Value

out An ExploratorySummarizedExperimentList object suitable for passing to prepare_app

Details

For a simple study with one 'experiement' for Gene-level results, and three 'assays' describing raw, filtered and normalised expression you might make a YAML like:

title: My RNA seq experiment
author: Joe Blogs
report: report.md
group_vars:
  - Group
  - Replicate
default_groupvar: Group
experiments:
  Gene:
    coldata:
      file: my.experiment.csv
      id: External
    annotation:
      file: my.annotation.csv
      id: gene_id
      entrez: ~
      label: gene_id
    expression_matrices:
      Raw:
        file: raw_counts.csv
        measure: counts
      Filtered:
        file: filtered_counts.csv
        measure: Counts per million
      Normalised:
        file: normalised_counts.csv
        measure: Counts per million
    read_reports:
      read_attrition: read_attrition.csv
contrasts:
  comparisons:
  - Variable: Group
    Group.1: control
    Group.2: TreatmentA
  - Variable: Group
    Group.1: control
    Group.2: TreatmentB
contrast_stats:
  Gene:
    Normalised:
      pvals: pvals.csv
      qvals: qvals.csv

Examples

eselist <- eselist_from_yaml("my.yaml")
#> Warning: cannot open file 'my.yaml': No such file or directory
#> Error in readLines(con, warn = readLines.warn): cannot open the connection