topLineEval: Evaluate cell lines

In Bin-Chen-Lab/octad: Open Cancer TherApeutic Discovery (OCTAD)

Evaluate cell lines

Description

Evaluate predictions using pharmacogenomics data. Given a cell line, the function computes the correlation between sRGES and drug sensitivity data taken from CTRP. A higher correlation means a better prediction. The cell line could be computed from computeCellLine.

Usage

  topLineEval(topline=NULL,mysRGES=NULL,outputFolder="")

Arguments

topline	list of cell lines to be used for prediction.
mysRGES	sRGES data.frame produced by runsRGES.
outputFolder	Path to store results.

Value

The function produces 3 feils in the output directory:

CellLineEval*_drug_sensitivity_insilico_results.txt	with drug sensitivity information.
*_auc_insilico_validation.html	correlation between drug AUC and sRGES in a related cell line.
*_ic50_insilico_validation.html	correlation between drug IC50 and sGRES in a related cell line.

See Also

runsRGES

Examples

#load example sRGES computed by runsRGES() function for HCC 
#vs liver adjacent tissues on octad.small dataset
data("sRGES_example",package='octad') #load example sRGES
#Pick up cell lines
topLineEval(topline = 'HEPG2',mysRGES = sRGES_example,outputFolder=tempdir())

Bin-Chen-Lab/octad documentation built on Jan. 28, 2023, 11:20 p.m.