score_conditions_vs_control: Scores conditions against a single control.

In HenryWard/orthrus: Scoring Combinatorial CRISPR Screens

Scores conditions against a single control.

Description

Scores guides for any number of condition screens against a control screen (e.g. for directly comparing drug response to DMSO response). Do NOT use this function if you would like to compare guides against a null model derived from single-gene effects. In that case, call score_combn_vs_single instead. After running this function, pass the resulting dataframe to call_condition_hits to call significant effects.

Usage

score_conditions_vs_control(
  guides,
  screens,
  control_screen_name,
  condition_screen_names,
  separate_orientation = FALSE,
  min_guides = 3,
  test = "moderated-t",
  loess = TRUE,
  fdr_method = "BY",
  filter_genes = NULL,
  return_residuals = TRUE,
  verbose = FALSE
)

Arguments

guides	A list of guides returned from split_guides.
screens	List of screens generated with add_screens.
control_screen_name	Name of a control screen to test condition screens against.
condition_screen_names	A list of condition screen names to score against the control screen.
separate_orientation	If true, then guide values are scored separately across each orientation (default FALSE).
min_guides	The minimum number of guides per gene pair required to score data (default 3).
test	Type of hypothesis testing to run. Must be one of "rank-sum" for Wilcoxon rank-sum testing or "moderated-t" for moderated t-testing (default "moderated-t").
loess	If true, loess-normalizes residuals before running hypothesis testing. Only works when test = "moderated-t" (default TRUE).
fdr_method	Type of FDR to compute. One of "BH", "BY" or "bonferroni" (default "BY").
filter_genes	List of genes to filter from scoring (default NULL).
return_residuals	If FALSE, returns NA instead of residuals dataframe (default TRUE). This is recommend if scoring large datasets and memory is a limitation.
verbose	If true, prints verbose output (default FALSE).

Value

A list containing two dataframes. The first entry, named "scored_data" in the list, contains scored data with separate columns given by the specified control and condition names. The second entry, named "residuals" in the list, is a dataframe containing control, condition and loess-normalized residuals for all guides.

HenryWard/orthrus documentation built on June 2, 2023, 10:28 p.m.