rna_coexpress: Perform RNA co-expression analysis

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Perform RNA co-expression analysis

Description

Performs multiple correlation coefficient analyses and determines cut to identify most likely co-expressed genes.

Usage

rna_coexpress(
  input_genes = NULL,
  input_disease = NULL,
  input_cell_lines = NULL,
  core_num = NULL,
  output_dir = NULL,
  data_dir = NULL,
  filename = NULL,
  test = FALSE
)

Arguments

input_genes	string, A vector containing one or more Hugo Symbol, Default: NULL
input_disease	string, A vector one or more disease contexts, Will perform pan-cancer analyses (all cell lines) by default, Default: NULL
input_cell_lines	string, A vector DepMap_IDs for which co-essentiality mapping will be performed on. Will perform pan-cancer analyses (all cell lines) by default, Default: NULL
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.
test	logical, TRUE/FALSE whether you want to run only a small subset (first 10 genes) to ensure function will run properly prior to running all 18,333 genes. Default: FALSE.

Details

Description of output data frame

• GeneNameID_A - Hugo symbol with NCBI gene ID of query gene.

• GeneNameID_B - Hugo symbol with NCBI gene ID of all genes targeted in the DepMap KO screen.

• estimate - Correlation coefficient output from ?cor.test.

• statistic - Pearson's correlation statistic. Output from ?cor.test.

• p.value - P-value from Pearson's correlation statistic. Output from ?cor.test.

• parameter - Degrees of freedom. Output from ?cor.test.

• Rank - Rank by correlation coefficient.

• Padj_BH - Benjamini-Hochberg adjusted p-value.

Value

A data frame containing Pearson correlation coefficients. 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(".")
}

## Not run: 
coess_df <- rna_coespress(
input_gene = 'ARID1A',
input_disease = 'Pancreatic Cancer',
core_num = 2,
data_dir = gretta_data_dir, 
output_dir = gretta_output_dir,
test = TRUE)

## End(Not run)

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