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


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Documentation for package ‘CompGO’ version 1.10.0

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annotateBedFromDb Annotate .bed file to genes
bed.sample A sample of 25 rows from a .bed file of mm9 regions
compareZscores Compare the Z scores of individual GO terms between two input annotation charts
doZtrans.single Z transform a single functional annotation chart from DAVID
gata4 A .bed file containing genomic ranges sampled from gata4
getFnAnot_genome Get the functional annotation chart of a gene list using DAVID
mef2a A .bed file containing genomic ranges sampled from mef2a
nkx25 A .bed file containing genomic ranges sampled from nkx25
p300 A .bed file containing genomic ranges sampled from p300
PCAplot Plot PCA given an input list of fnAnot charts
plotDendrogram Plot dendrogram given an input list of fnAnot charts
plotInteractive Interactive plotting function for groups of GO terms
plotPairwise Generates a scatterplot of two sets of GO terms based on DAVID P-values
plotTwoGODags Plots a directed acyclic graph of GO terms from two different sources
plotZRankedDAG Plot a directed acyclic graph (DAG) based on the corrected Pvalues generated from comparing two sets of Z scores.
plotZScores Performs z transform on two sets of GO terms and plots scatterplot of result
slidingJaccard Plot two functional annotation charts using a sliding Jaccard coefficient
srf A .bed file containing genomic ranges sampled from srf
tbx5 A .bed file containing genomic ranges sampled from tbx5
viewKegg Compare KEGG pathways between two functional annotation charts
zTransformDirectory Z-score transformation of DAVID functional annotation charts in a supplied directory