Description Usage Arguments Value See Also Examples
View source: R/octadDrugEnrichment.R
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.
1 | octadDrugEnrichment(sRGES=NULL,target_type='chembl_targets',enrichFolder='enrichFolder')
|
sRGES |
sRGES data frame produced by |
target_type |
one or several of |
enrichFolder |
folder to store output. |
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 |
|
1 2 3 4 5 6 7 8 9 10 11 | 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'))
|
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