bed.sample

25 regions from a .bed file for use in example code, contains regions from mm9

datasets

This package contains functions to accomplish several tasks. It is
able to download full genome databases from UCSC, import .bed files easily,
annotate these .bed file regions with genes (plus distance) from
aforementioned database dumps, interface with DAVID to create functional
annotation and gene ontology enrichment charts based on gene lists (such as
those generated from input .bed files), statistically compare gene ontology
enrichment between multiple experiments and finally visualise and compare
these enrichments using directed acyclic graphs or scatterplots. CompGO also
enables clustering of experiments based on their GO profiles and provides
functions for performing and visualising principle component analysis.

Ashley J. Waardenberg

CompGO

An R pipeline for .bed file annotation, statistical comparison of GO term
enrichment between gene sets and data visualisation

bed.sample function

A data.frame with 25 obs. of 3 variables: chromosome, start position, end position

bed.sample: A sample of 25 rows from a .bed file of mm9 regions

Description

Usage

Arguments

Format