R/calculate_MiniMax_statistic.R
MiniMax_calculateStatistic.RdGiven a data frame of pathway-level p-values, calculate the MiniMax statistic (but not the significance level of this statistic).
MiniMax_calculateStatistic(res_df, orderStat = 2L)
| res_df | A data frame of p-values. The rows correspond to gene sets / pathways and the columns correspond to a data platform for the disease of interest. |
|---|---|
| orderStat | How many platforms should show a biological signal for a pathway / gene set to have multi-omic "enrichment"? Defaults to 2. See "Details" for more information. |
A vector of the MiniMax statistic values.
The MiniMax statistic is defined as the minimum of all pairwise
maxima of pathway p-values. This operation is arithmetically
equivalent to sorting the p-values and taking the second smallest.
In our experience, setting this "order statistic" cutoff to 2 is
appropriate for =< 5 data platforms. Biologically, this is equivalent to
saying "if this pathway is dysregulated in at least two data types for
this disease / condition, it is worthy of additional consideration". In
situations where more than 5 data platforms are available for the disease
of interest, we recommend increasing the orderStat value to 3.
MiniMax_calculateStatistic(multiOmicsHighSignalResults_df[, -(1:2)]) #> [1] 0.757 0.701 0.697 0.000 0.000 0.687 0.688 0.326 0.275 0.423 0.240 0.706 #> [13] 0.548 0.561 0.538 0.000 0.475 0.684 0.000 0.370 0.586 0.725 0.478 0.031 #> [25] 0.647 0.101 0.391 0.756 0.482 0.509 0.468 0.027 0.725 0.518 0.225 0.524 #> [37] 0.269 0.316 0.720 0.117 0.553 0.411 0.314 0.879 0.210 0.519 0.766 0.618 #> [49] 0.152 0.000