Summarize gene set enrichment tests

Returns a data.table with one row per gene set. This data.table contains columns:

set

name of gene set

cond_Z

Z statistic for continuous component

cont_P

wald P value

cont_effect

difference in continuous regression coefficients between null and test sets (ie, the numerator of the Z-statistic.)

disc_Z

Z statistic for discrete

disc_P

wald P value

disc_effect

difference in discrete regression coefficients between null and test sets.

combined_Z

combined discrete and continuous Z statistic using Stouffer's method

combined_P

combined P value

combined_adj

FDR adjusted combined P value

# S4 method for GSEATests
summary(object, ...)

Arguments

object

A GSEATests object

...

passed to calcZ

Value

data.table

See also

gseaAfterBoot

Examples

## See the examples in gseaAfterBoot
example(gseaAfterBoot)
#> 
#> gsAftB> data(vbetaFA)
#> 
#> gsAftB> vb1 = subset(vbetaFA, ncells==1)
#> 
#> gsAftB> vb1 = vb1[,freq(vb1)>.1][1:15,]
#> 
#> gsAftB> zf = zlm(~Stim.Condition, vb1)
#> 
#> Done!
#> 
#> gsAftB> boots = bootVcov1(zf, 5)
#> 
#> gsAftB> sets = list(A=1:5, B=3:10, C=15, D=1:5)
#> 
#> gsAftB> gsea = gseaAfterBoot(zf, boots, sets, CoefficientHypothesis('Stim.ConditionUnstim'))
#> 
#> gsAftB> ## Use a model-based estimate of the variance/covariance.
#> gsAftB> gsea_mb = gseaAfterBoot(zf, boots, sets, CoefficientHypothesis('Stim.ConditionUnstim'),
#> gsAftB+ control = gsea_control(var_estimate = 'modelbased'))
#> 
#> gsAftB> calcZ(gsea)
#> , , metric = Z
#> 
#>    comp
#> set       cont      disc
#>   A -1.7031548 -1.074742
#>   B -0.7446833 -4.273887
#>   C        NaN -3.954742
#>   D -1.7031548 -1.074742
#> 
#> , , metric = P
#> 
#>    comp
#> set      cont        disc
#>   A 0.1270547 0.319242117
#>   B 0.4948398 0.002754653
#>   C       NaN 0.005470883
#>   D 0.1270547 0.319242117
#> 
#> 
#> gsAftB> summary(gsea)
#> 
#> gsAftB> ## Don't show: 
#> gsAftB> stopifnot(all.equal(gsea@tests['A',,,],gsea@tests['D',,,]))
#> 
#> gsAftB> stopifnot(all.equal(gsea@tests['C','cont','stat','test'], coef(zf, 'C')[15,'Stim.ConditionUnstim']))
#> 
#> gsAftB> ## End(Don't show)
#> gsAftB> 
#> gsAftB> 
#> gsAftB>