topLineEval: Evaluate cell lines

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

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,mysRGES)

Arguments

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

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

#select samples
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary') #select data
case_id=HCC_primary$sample.id #select cases
HCC_adjacent=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'adjacent'&data.source == 'TCGA') #select data
control_id=HCC_adjacent$sample.id #select cases
#compute DE
res=diffExp(case_id,control_id,source='octad.small',output=TRUE)
res=subset(res,abs(log2FoldChange)>2&padj<0.001)
#Compute sRGES
#sRGES=runsRGES(res,max_gene_size=50)
#Pick up cell lines
#topLineEval(topline = c('HEPG2'),mysRGES = sRGES)

Bin-Chen-Lab/octad_desktop documentation built on Oct. 28, 2020, 11:13 a.m.