getPvals.Rd
With null distributions estimated using the generateNull()
function, p-values are estimated using a one-tailed test. A minimum p-value
of 1/B can be achieved with B permutations.
getPvals(permuteResult, scoredf)
permuteResult | A matrix, null distributions for each sample generated
using the |
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scoredf | A dataframe, the scored results of samples under test
generated using the |
Estimated p-values for enrichment of the signature in each sample. A p-value of 1/B indicates that the estimated p-value is less than or equal to 1/B.
ranked <- rankGenes(toy_expr_se) scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn) # find out what backends can be registered on your machine BiocParallel::registered()#> $MulticoreParam #> class: MulticoreParam #> bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB #> bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE #> bptimeout: 2592000; bpprogressbar: FALSE #> bpRNGseed: 1 #> bplogdir: NA #> bpresultdir: NA #> cluster type: FORK #> #> $SnowParam #> class: SnowParam #> bpisup: FALSE; bpnworkers: 44; bptasks: 0; bpjobname: BPJOB #> bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE #> bptimeout: 2592000; bpprogressbar: FALSE #> bpRNGseed: #> bplogdir: NA #> bpresultdir: NA #> cluster type: SOCK #> #> $SerialParam #> class: SerialParam #> bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB #> bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE #> bptimeout: 2592000; bpprogressbar: FALSE #> bplogdir: NA #># the first one is the default backend, and it can be changed explicitly. # See vignette for more details permuteResult = generateNull(upSet = toy_gs_up, downSet = toy_gs_dn, ranked, B =10, seed = 1, useBPPARAM = NULL) # call the permutation function to generate the empirical scores # for B times. pvals <- getPvals(permuteResult,scoredf)