% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.R
\title{Create path results table with highest significant GO ancestors}
paths_to_go_ancestor(pathways, comp_paths, comp_go, pval = 0.05)
\item{pathways}{Pathways object}

\item{comp_paths}{Wilcoxon comparison of the matrix of pathways values
as returned by \code{do_wilcoxon}.}

\item{comp_go}{Wilcoxon comparison of the matrix of GO values as
returned by \code{do_wilcoxon}.}

\item{pval}{P-value cut-off. Default values is set to 0.05.}
Table of comparisons with Highest common ancestors
Create table of results with the comparison of the paths together with
the GO functional annotation and the highest significant GO ancestor
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 \code{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.
sample_group <- brca_design[colnames(path_vals),"group"]
comp_go <- do_wilcoxon(go_vals, sample_group, g1 = "Tumor", g2 = "Normal")
\dontrun{pathways <- load_pathways(species = "hsa", pathways_list =
c("hsa03320", "hsa04012"))
table <- paths_to_go_ancestor(pathways, comp, comp_go)}