score_conditions_batch: Scores multiple conditions against multiple controls
In HenryWard/orthrus: Scoring Combinatorial CRISPR Screens

score_conditions_batch

R Documentation

Scores multiple conditions against multiple controls

Description

Takes in an input .tsv file with two columns for "Screen" and "Control" and scores all screens listed in "Screen" against their corresponding screens listed in "Control." Outputs all files and plots in the specified folder.

Usage

score_conditions_batch(
  guides,
  screens,
  batch_table,
  output_folder,
  separate_orientation = FALSE,
  min_guides = 3,
  test = "moderated-t",
  loess = TRUE,
  filter_genes = NULL,
  fdr_method = "BY",
  fdr_threshold = 0.1,
  differential_threshold = 0.5,
  neg_type = "Negative",
  pos_type = "Positive",
  plot_type = "png"
)

Arguments

`guides`	A list of guides returned from `split_guides`.
`screens`	List of screens generated with `add_screens`.
`batch_table`	Either a dataframe or a path to .tsv file mapping screens to their controls for scoring, with two columns for "Screen" and "Control." Screens to score against derived null-models with the combn scoring mode must have their respective control labeled as "combn."
`output_folder`	Folder to output scored data and plots to.
`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).
`filter_genes`	List of genes to filter from scoring (default NULL).
`fdr_method`	Type of FDR to compute. One of "BH", "BY" or "bonferroni" (default "BY")
`fdr_threshold`	Threshold below which to call gene effects as significant (default 0.1).
`differential_threshold`	Absolute value threshold on differential effects, below which gene effects are not called as significant (default 0.5).
`neg_type`	Label for significant effects with a negative differential effect (default "Negative").
`pos_type`	Label for significant effects with a positive differential effect (default "Positive").
`plot_type`	Type of plot to output, one of "png" or "pdf" (default "png").