identifySLHits: Retrieve list of mutation-specific synthetic lethal partners...

In cbg-ethz/slidr: Discovery of mutation-specific synthetic lethal partners from large pan-cancer perturbation screens

Retrieve list of mutation-specific synthetic lethal partners for each type of cancer

Description

Rank test based on Irwin-Hall distribution to identify synthetic lethal (SL) partners in the mutated samples. The function also performs a two sided wilcoxon or t-test on the wild type samples to give a p-value required for filtering.

Usage

identifySLHits(
  canc_data,
  fp_thresh = 1,
  path_results = NULL,
  WT_pval_thresh = 0.1
)

Arguments

canc_data	Processed data object for a given cancer type
fp_thresh	The average number of false positives allowed. Default = 1
path_results	The path to where the results should be stored. Default working directory.
WT_pval_thresh	Discard SL pairs with WT p-values less than this threshold. Default = 0.1 Required by 'plotSLBoxplot' function

Value

a dataframe of driver gene with its corresponding SL partner, the p-value in WT samples, p-value in mutated samples, the corresponding value after scaling, and available drugs if any.

cbg-ethz/slidr documentation built on Feb. 8, 2023, 11:15 p.m.