---
title: "hpAnnot"
date: "`r Sys.Date()`"
output: BiocStyle::pdf_document
vignette: >
    %\VignetteIndexEntry{hpAnnot}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
author:
- name: Marta R. Hidalgo
  affiliation: Unidad de Bioinformática y Bioestadística, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain
  email: marta.hidalgo@outlook.es
- name: Francisco Salavert
  affiliation: BioBam Bioinformatics S.L., Valencia, 46012, Spain
- name: Alicia Amadoz
  affiliation: Department of Bioinformatics, Igenomix S.A., Valencia, 46980, Spain
- name: Çankut Cubuk
  affiliation: Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain
- name: José Carbonell-Caballero
  affiliation: Chromatin and Gene expression Lab, Gene Regulation, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona, 08003, Spain
- name: Joaquín Dopazo
  affiliation: 
  - Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, 41013, Spain 
  - Functional Genomics Node (INB), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain. 
  - Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Sevilla, 41013, Spain
abstract: >
    _HpAnnot_ is the annotation and data package of the _hipathia_ package.
    _Hipathia_ is a method for the computation of signal transduction along
    signaling pathways. The method is based on an iterative algorithm which
    is able to compute the signal intensity passing through the nodes of a
    network by taking into account the level of expression of each gene and
    the intensity of the signal arriving to it.

---


\section{Usage}

In order to access to the files stored in `r Biocpkg("AnnotationHub")`, type:

```{r, fig.show='hold', message=FALSE, warning=FALSE}
library(AnnotationHub)
ah <- AnnotationHub()
hp <- query(ah, "hpAnnot")
hp
mcols(hp)[,c("title", "description")]
xtabs(~dataprovider + species, mcols(hp))
head(hp[["AH60887"]])
hp$title
```

For further information on this please refer to `r Biocpkg("AnnotationHub")`.
