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Wrapper function for the DIALOGUE refinement parameters

params_dialogue_refine.Rd

Stage three of DIALOGUE: the cross-partner meta-analysis that decides which genes survive, and the non-negative refit of the programme scores onto them.

Usage

params_dialogue_refine(
  support_p = 0.1,
  min_support_fraction = 0.333333333333333,
  min_stratum = 5L,
  early_stop_cor = 0.95,
  permissive_p = 0.001,
  strict_p = 0.05
)

Arguments

support_p

Numeric. Adjusted p below which one partner counts as supporting a gene. Must be in (0, 1]. Defaults to 0.1.

min_support_fraction

Numeric. Minimum supporting fraction for a stratum to enter the staged fit. Must be in [0, 1]. Defaults to 0.3333333333333333.

min_stratum

Integer. Minimum genes in a stratum before it is worth fitting. Defaults to 5L.

early_stop_cor

Numeric. Correlation between the original score and the running fit at which the staged fit stops early. Must be in (0, 1]. Defaults to 0.95.

permissive_p

Numeric. Fisher-combined p for the permissive gene list, where a gene is carried by partner support rather than by a positive coefficient. Must be in (0, 1]. Defaults to 0.001.

strict_p

Numeric. Fisher-combined p for the strict gene list, which also demands that every partner supports the gene. Must be in (0, 1]. Defaults to 0.05.

Value

A named list with the following elements:

  • support_p - Numeric. Adjusted p below which one partner counts as supporting a gene. Must be in (0, 1]. Defaults to 0.1.

  • min_support_fraction - Numeric. Minimum supporting fraction for a stratum to enter the staged fit. Must be in [0, 1]. Defaults to 0.3333333333333333.

  • min_stratum - Integer. Minimum genes in a stratum before it is worth fitting. Defaults to 5L.

  • early_stop_cor - Numeric. Correlation between the original score and the running fit at which the staged fit stops early. Must be in (0, 1]. Defaults to 0.95.

  • permissive_p - Numeric. Fisher-combined p for the permissive gene list, where a gene is carried by partner support rather than by a positive coefficient. Must be in (0, 1]. Defaults to 0.001.

  • strict_p - Numeric. Fisher-combined p for the strict gene list, which also demands that every partner supports the gene. Must be in (0, 1]. Defaults to 0.05.

Details

Two gene lists come out. The permissive one asks only for a Fisher-combined p below permissive_p; the strict one is looser on the p-value but also demands that every partner supports the gene. They are not nested by threshold, they are nested by evidence, and the strict list is the one to quote.

References

Jerby-Arnon & Regev, Nature Biotechnology, 2022