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OpenReadout

summarize

summarize computes group statistics of a table written earlier by batch -o or by --tidy -o, or of any CSV, TSV, JSON Lines, JSON or Parquet table: n, mean, sd, sem, median, min, max and CV % per group.

openreadout summarize [OPTIONS] --by <COLUMNS> <TABLE>

MCP: openreadout_summarize.

Flags

  • --by COLUMNS: summarize by these columns, comma-separated or repeated. Channels, parameters and populations stay apart unless --exact-by.
  • --value COLUMNS: value columns to summarize. Default: the measure’s main values.
  • --replicate COLUMN: average the rows of each replicate before summarizing; n then counts replicates.
  • --test welch|mann-whitney: compare each group with the control.
  • --control VALUE: the control group, a value of the first --by column.
  • --where COLUMN=VALUE: keep only matching rows (!= to leave them out). Repeatable.
  • --exact-by: group by exactly --by, without adding the measurement columns that vary.
  • -o, --output FILE: also write the summary as .csv, .tsv, .jsonl, .json or .parquet. The write is verified.
  • --overwrite: replace an existing output file.
  • --csv: print the summary as CSV.
  • --json: print the JSON wrapper instead of text.

Example

Terminal window
openreadout batch peaks runs/ -r --sample-sheet samples.csv -o rows.parquet
openreadout summarize rows.parquet --by condition --test welch --control DMSO

The Batch tables guide explains group summaries and tests.

JSON

summarize.

Run openreadout summarize --help for the full help of your installed version.