View source: R/enrichment_functions.R

combinePvalues | R Documentation |

This function applies the Stouffer method, the Edgington method or the Fisher\'s combined probability test to combine p-values of independent tests that are based on the same null hypothesis. The Stouffer method can also be applied in a weighted fashion.

```
combinePvalues(df, method = "stouffer", weights = NULL)
```

`df` |
Data frame where rows represent a certain pathway or gene set and columns represent p-values derived from independent tests, e.g., different omics layer. |

`method` |
String that specifies the method to combine multiple p-values. Default: "stouffer" Options: "stouffer", "fisher", "edgington" |

`weights` |
List of weights that will be used in a weighted Stouffer method. |

Vector of length `nrow(df)`

with combined p-values.

```
df <- cbind(runif(5), runif(5), runif(5))
colnames(df) <- c("trans.pval", "prot.pval", "meta.pval")
# run the unweighted summation of z values
combinePvalues(df)
# run the weighted variant
combinePvalues(df, weights = c(10, 5, 1))
# run the Fisher's combined probability test
combinePvalues(df, method = "fisher")
# run the Edgington's method
combinePvalues(df, method = "edgington")
```

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