Optimized Functional Annotation Of ChIP-seq Data


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Documentation for package ‘geneXtendeR’ version 1.10.0

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allPeakLengths Produces box-and-whisker plot showing distribution of peak lengths across a peaks input file.
annotate Annotate peaks file.
annotate_n Annotate peaks file.
barChart Produces bar charts.
cumlinePlot Produces cumulative line plots.
diffGO Finds differential gene ontologies
distinct Finds unique genes under peaks.
gene_annotate Annotate peak file based on gene.
gene_lookup Looks up specific gene and closest peaks
hotspotPlot Graphs hotspots of statistically significant peak activity.
linePlot Produces line plots.
makeNetwork Makes gene-GO networks
makeWordCloud Makes word cloud from gene ontology terms
meanPeakLength Calculates mean (average) peak length for any genomic region.
meanPeakLengthPlot Produces line plots of mean (average) peak length within any genomic interval.
peakLengthBoxplot Produces box-and-whisker plot of peak lengths within any genomic interval.
peaksInput Preprocesses a peaks input file.
peaksMerge Transform peaks into merged peaks.
plotWordFreq Plots word frequencies found within gene ontology terms
rat Gene transfer format (GTF) file for rat (Rattus_norvegicus.Rnor_6.0.84)
samplepeaksinput Sample peaks list to be used as input to geneXtendeR