annotate_df: Combine and annotate co-essential or co-expression dataframe

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Combine and annotate co-essential or co-expression dataframe

Description

Combines and annotates co-essential data frame with inflection points to determine which genes are likely to be candidates co-essential genes.

Usage

annotate_df(
  input_df = NULL,
  input_inflec = NULL,
  top_n = NULL,
  use_inflection = TRUE
)

Arguments

input_df	data frame, A data frame output from coessential_map(), rna_express(), and protein_express(), Default: NULL
input_inflec	data frame, A data frame output from get_inflection_points(), Default: NULL
top_n	vector, The number of top/bottom candidates to select (eg. if 10 there will be top top co-essential and 10 anti-essential genes), Default: NULL
use_inflection	logical, TRUE to use inflection points as threshold in input_inflec or FALSE to use top_n as cutoff , Default: TRUE

Details

Description of output data frame

• Candidate_gene - Logical; Whether the coefficient had a p-value < 0.05 and was at or above (positive curve) or below (negative curve) of the inflection point.

• See ?coessential_map for details.

Value

The input data frame containing co-essential correlation coefficients will be annotated with an additional column Candidate_gene to indicate whether the gene is considered to a possible co-essential gene.

Examples

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

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

load(paste0(
gretta_data_dir,'/sample_22Q2_ARID1A_coessential_result.rda'), 
envir = environment())
load(paste0(
gretta_data_dir,'/sample_22Q2_ARID1A_coessential_inflection.rda'), 
envir = environment())

annotated_df <- annotate_df(coess_df, coess_inflection_df)

ytakemon/GINIR documentation built on Feb. 27, 2024, 1:33 p.m.