store_results: Store output to Synapse
In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

store_results

R Documentation

Store output to Synapse

Description

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

Usage

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.