Carry out set enrichment test based on hyper-geometric distribution

hyperEnrichment(
  drawn,
  categories,
  ntotal = length(unique(unlist(categories))),
  min.drawsize = 4,
  mht = TRUE,
  verbose = TRUE
)

Arguments

drawn	One or more sets of 'drawn' items (e.g., genes). Basically, a list of signatures.
categories	list of gene sets (e.g., MSigDB c2)
ntotal	background population, i.e., the total no. of items from which items are supposed to have been drawn
min.drawsize	min no. of drawn items that must be among categories' items
mht	correct for multiple hypothesis testing across multiple 'draws'

Value

a data.frame with rows indexed by the signature(s) tested

Examples


# load objects hyperSig (a list of signatures) and hyperGsets (a GeneSet object)
# and run hyper-enrichment test

data(hyper) # contains objects hyperSig and hyperGsets
hyperE <- hyperEnrichment(drawn=hyperSig,categories=getGeneSet(hyperGsets),ntotal=10000)
#> Testing 10 drawsets on 1320 categories and 8428 total items ..
#> *** Testing control.UP .. 4/11 annotated genes found (min fdr: 1)
#> *** Testing control.DN .. 8/23 annotated genes found (min fdr: 0.69)
#> *** Testing TAZ.UP .. 15/41 annotated genes found (min fdr: 1)
#> *** Testing TAZ.DN .. 17/35 annotated genes found (min fdr: 1)
#> *** Testing YAP.UP .. 164/356 annotated genes found (min fdr: 5.9e-09)
#> *** Testing YAP.DN .. 261/470 annotated genes found (min fdr: 6.5e-49)
#> *** Testing TAZ+YAP.UP .. 60/166 annotated genes found (min fdr: 1)
#> *** Testing TAZ+YAP.DN .. 186/381 annotated genes found (min fdr: 1.2e-12)
#> *** Testing DPAGT1.UP .. 15/70 annotated genes found (min fdr: 1)
#> *** Testing DPAGT1.DN .. 67/199 annotated genes found (min fdr: 1)
#> done.
#> MHT-correction across multiple draws ..done.
#> Categories tested: 1320
#> Candidate sets:      10
#> Sets tested:         10
#> Items tested:      1752 (min,med,max: 11,118,470)
#> N(FDR<=0.25):        78
#> N(FDR<=0.05):        48
#> N(FDR<=0.01):        26
head(hyperE)
#>      set          pval    fdr                 set annotated set size
#> [1,] "control.UP" "0.012" "0.971779141104295" "1"           "11"    
#> [2,] "control.UP" "0.013" "1"                 "1"           "11"    
#> [3,] "control.UP" "0.023" "1"                 "1"           "11"    
#> [4,] "control.UP" "0.027" "1"                 "1"           "11"    
#> [5,] "control.UP" "0.027" "1"                 "1"           "11"    
#> [6,] "control.UP" "0.031" "1"                 "1"           "11"    
#>      category annotated total annotated
#> [1,] "11"               "10000"        
#> [2,] "12"               "10000"        
#> [3,] "21"               "10000"        
#> [4,] "25"               "10000"        
#> [5,] "25"               "10000"        
#> [6,] "29"               "10000"        
#>      category                                                                  
#> [1,] "PID_ALK2PATHWAY"                                                         
#> [2,] "REACTOME_CS_DS_DEGRADATION"                                              
#> [3,] "REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS"                               
#> [4,] "PID_TOLL_ENDOGENOUS_PATHWAY"                                             
#> [5,] "REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS"
#> [6,] "PID_INTEGRIN2_PATHWAY"                                                   
#>      hits   
#> [1,] "BMP7" 
#> [2,] "BGN"  
#> [3,] "BGN"  
#> [4,] "BGN"  
#> [5,] "BGN"  
#> [6,] "SPON2"