Store output to Synapse — store

Store transformed data, markdown and html report to a Folder in Synapse.

store_results(
  clean_md = clean_md,
  filtered_counts = filtered_counts,
  biomart_results = biomart_results,
  cqn_counts = cqn_counts$E,
  de_results = de,
  residualized_counts = residualized_counts,
  report = report,
  syn_names,
  data_names,
  parent_id,
  inputs,
  activity_provenance,
  rownames = NULL,
  config_file = NULL,
  report_name = NULL
)

Arguments

clean_md: The target containing the metadata data frame. Defaults to target name constrained by "targets::tar_make".
filtered_counts: The target containing counts after low gene expression has been removed. Defaults to target name constrained by "targets::tar_make()".
biomart_results: The target containing gene annotations from biomart. Defaults to target name constrained by "targets::tar_make".
cqn_counts: The target containing Conditional Quantile Normalized (CQN) counts. Defaults to target name constrained by "targets::tar_make".
de_results: The target containing differential expression gene lists. Defaults to target name constrained in the _targets.R file.
residualized_counts: The target containing counts adjusted for batch effects. Defaults to target name constrained in the _targets.R file.
report: The target containing the rendered html document. Defaults to target name constrained in the _targets.R file.
syn_names: A list of human-readable names for the Synapse entities ordered by `metadata`, `filtered_counts`, `biomart_results`, `cqn_counts`.
data_names: A list of identifiers to embed in the file name ordered by `clean_md`, `filtered_counts`, `biomart_results`, `cqn_counts`, `de_results`.
parent_id: A Synapse Id that corresponds to a project or folder to store output.
inputs: A character vector of Synapse Ids to create provenance between output files and input files.
activity_provenance: A phrase to describe the data transformation for provenance.
rownames: A list of variables to store rownames ordered by `metadata`, `filtered_counts`, `biomart_results`, `cqn_counts`. If not applicable, set as NULL.
config_file: Optional. Path to configuration file.
report_name: Name of output markdown file.