GI_screen_perms: Perform permutation test n genetic interaction screen

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Perform permutation test n genetic interaction screen

Description

Randomly samples dependency probabilities from a given mutant and control group screened.

Usage

GI_screen_perms(
  control_id = NULL,
  mutant_id = NULL,
  n_perm = 100,
  core_num = NULL,
  output_dir = NULL,
  data_dir = NULL,
  filename = NULL
)

Arguments

control_id	string, A vector containing two or more DepMap_id, Default: NULL
mutant_id	string, A vector containing two or more DepMap_id, Default: NULL
n_perm	integer, Number of permutations to run, Default: 100
core_num	integer, Number of cores to run analysis, Default: NULL
output_dir	string, Full path to where output file should be saved, Default: NULL
data_dir	string Path to GRETTA_data
filename	string name of file without the '.csv' extension.

Details

Description of output data frame

• perm_test - permutation iteration

• ⁠_median⁠, ⁠_mean⁠ - Control and mutant group's median, mean, of dependency probabilities. Dependency probabilities range from zero to one, where one indicates a essential gene (ie. KO of gene was lethal) and zero indicates a non-essential gene (KO of gene was not lethal)

• Pval - P-value from Mann Whitney U test between control and mutant groups.

• n_perm - Number of permutations assigned

Value

A data frame containing results from the genetic screen. A copy is also saved to the directory defined in output_dir.

Examples

gretta_data_dir <- './GRETTA_example/'
gretta_output_dir <- './GRETTA_example_output/'

if(!dir.exists(gretta_data_dir)){
  download_example_data(".")
}

if(!dir.exists(gretta_data_dir)){
  download_example_data(".")
}

Screen_results <- GI_screen_perms(
control_id = c('ACH-001354', 'ACH-000274', 'ACH-001799'), 
mutant_id = c('ACH-000911', 'ACH-001957', 'ACH-000075'), 
n_perm = 10,
core_num = 2, 
output_dir = gretta_output_dir,
data_dir = gretta_data_dir)

ytakemon/GINIR documentation built on Dec. 17, 2024, 7:39 a.m.