probes2pathways: Extract pathways from "exemplars"

In asakellariou/git-git.bioconductor.org-packages-mAPKL: A Hybrid Feature Selection method for gene expression data

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)

asakellariou/git-git.bioconductor.org-packages-mAPKL documentation built on June 5, 2019, 8:49 p.m.