octadDrugEnrichment: Compute Drug enrichment

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

Description

Perform enrichment analysis of drug hits based on chemical structures, drug-targets, and pharmacological classifications. An enrichment score calculated using ssGSEA and a p-value computed through a permutation test are provided.

Usage

  octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder')

Arguments

sRGES	sRGES data frame produced by runsRGES.
target_type	one or several of 'chembl_targets','mesh','ChemCluster' databases selected. By deafult only 'chembl_targets' will be used.
enrichFolder	folder to store output.

Value

Following files are created: enriched_*_targets.csv and top_enriched_*_*_targets.pdf. In the case of chemical structural analysis, additional files are created: *drugstructureClusters.csv and *misc.csv. The results provide useful information for following candidate selection and experimental design. For example, if two structurally similar drugs are both predicted as top hits, the chance of each drug as a true positive is high.

exprData

matrix with either log2 corrected counts or tmp matrix for selected samples.

See Also

runsRGES

Examples

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
res=diffExp(case_id,control_id,source='octad.small',output=TRUE)
res=subset(res,abs(log2FoldChange)>2)
#run sRGES computation
sRGES = runsRGES(dz_signature=res)
#run drug enrichment 
octadDrugEnrichment(sRGES = sRGES, target_type = c('chembl_targets','mesh',
                      'ChemCluster'))

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