topLineEval: Evaluate cell lines

View source: R/topLineEval.R

topLineEvalR Documentation

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, 12:04 p.m.