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,
  pattern = 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.

pattern

optional character suffix pattern used to match dataset filenames before the trailing .rds. Use "" to match all RDS files.

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,
  pattern = "carnation"
)