probes2pathways {mAPKL} | R Documentation

## Extract pathways from "exemplars"

### Description

The user may extract the pathways where the "exemplars" are involved with the aid of the reactome database.

### Usage

        probes2pathways(annotObj)

### Arguments

`annotObj` | The "Annot" class object.

### Details

This function utilizes the "Annot" class object as returned by the "annotate" function to extract the pathways where the "exemplars" are involved with the aid of the "reactome" database. We employ the probe Ids for the matching.

### Author(s)

Argiris Sakellariou

### Examples

    ## We use the "exemplars" from the mAPKL.Rd example

    exemplrs <- c(24, 26, 42, 45, 63, 81, 95, 99, 102, 113, 134, 135, 145, 152, 168)
    names(exemplrs)<- c("215717_s_at", "1561358_at", "222752_s_at", "233922_at",
    "218871_x_at", "33323_r_at", "244311_at", "220932_at", "205508_at", "209596_at",
    "215180_at", "1560638_a_at", "201852_x_at", "229947_at", "221731_x_at")

    gene.info <- annotate(exemplrs,"hgu133plus2.db")

    ## We now use the "gene.info" to identify the relevant pathways

    probes2pathways(gene.info)

[Package mAPKL version 1.16.0 Index]