Set config

This function updates a limited subset of the package config YAML. Only stable user-facing settings are writable; style settings and other internal options are intentionally left untouched.

Usage

set_config(
  config_path = get_config_path(),
  de_analysis = NULL,
  fdr_threshold = NULL,
  log2fc_threshold = NULL,
  max_upload_size = NULL,
  cores = NULL
)

Arguments

config_path

character path to the config YAML file to update. Defaults to the local config returned by get_config_path(). If the file does not exist yet, it is initialized from the bundled package config.

de_analysis

optional list with DE analysis config updates. Currently only de_analysis$column_names is supported, and the provided aliases are merged into the existing column-name mappings.

fdr_threshold

optional numeric FDR threshold between 0 and 1.

log2fc_threshold

optional numeric log2 fold-change threshold greater than or equal to 0.

max_upload_size

optional positive numeric upload limit in MB.

cores

optional positive integer number of cores to use.

Value

Updated config list, invisibly.

Examples

cfg_out <- tempfile(fileext = ".yaml")

set_config(
  config_path = cfg_out,
  de_analysis = list(
    column_names = list(
      padj = "qvalue",
      log2FoldChange = c("logFC", "avg_log2FC")
    )
  ),
  fdr_threshold = 0.05,
  log2fc_threshold = 1,
  max_upload_size = 50,
  cores = 2
)
#> Error in set_config(config_path = cfg_out, de_analysis = list(column_names = list(padj = "qvalue",     log2FoldChange = c("logFC", "avg_log2FC"))), fdr_threshold = 0.05,     log2fc_threshold = 1, max_upload_size = 50, cores = 2): could not find function "set_config"