paths_to_go_ancestor {hipathia} | R Documentation

## Create path results table with highest significant GO ancestors

### Description

Create table of results with the comparison of the paths together with the GO functional annotation and the highest significant GO ancestor (HSGOA).

### Usage

    paths_to_go_ancestor(pathways, comp_paths, comp_go, pval = 0.05)

### Arguments

`pathways` | Pathways object
`comp_paths` | Wilcoxon comparison of the matrix of pathways values as returned by `do_wilcoxon`.
`comp_go` | Wilcoxon comparison of the matrix of GO values as returned by `do_wilcoxon`.
`pval` | P-value cut-off. Default values is set to 0.05.

### Details

The table returns in each row: the name of a pathway and its Wilcoxon comparison information (direction, adjusted p-value), the GO term to which the path is related (not necessarily unique), the Wilcoxon comparison informationfor this GO (direction, adjusted p-value), the HSGOA of this GO and its Wilcoxon comparison information (direction, adjusted p-value).

The HSGOA is computed as the GO term with minimum level from all the significant (with respect to value `pval`) ancestors of a GO. The level of a GO term is computed as the number of nodes in the shortest path from this GO term to the term "GO:0008150". The ancestors of a node are defined as all the nodes from which a path can be defined from the ancestor to the node.

### Value

Table of comparisons with Highest common ancestors

### Examples

    data(comp)
    data(go_vals)
    data(brca_design)
    data(path_vals)
    sample_group <- brca_design[colnames(path_vals),"group"]
    comp_go <- do_wilcoxon(go_vals, sample_group, g1 = "Tumor", g2 = "Normal")
    ## Not run: pathways <- load_pathways(species = "hsa", pathways_list =
    c("hsa03320", "hsa04012"))
    table <- paths_to_go_ancestor(pathways, comp, comp_go)
    ## End(Not run)

[Package hipathia version 2.4.0 Index]