compEpiTools-package {compEpiTools} | R Documentation

## Tools for computational epigenomics

### Description

Tools for computational epigenomics

### Details

Package: | compEpiTools
Type: | Package
Version: | 0.1
Date: | 2014-04-07
License: | GPL
Depends: | methods

The package offers the following functionalities, divided by topic

Counting reads in GRanges:

- GRbaseCoverage: based on a GRanges and a BAM file, returns a list of base coverage vectors for each range

- GRcoverage: based on a GRanges and a BAM file, returns the total coverage for each range

- GRcoverageInbins: same as GRcoverage but dividing each range in equally-sized bins

- GRcoverageSummit: based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range

- GRenrichment: determines the enrichment over a set of genomic regions given two BAM files

- countOverlapsInBins: given a query and a subject GRanges returns a matrix of counts of subject in bins of query

- stallingIndex: computes the PolII stalling index based on number of ChIP-seq reads in promoter and genebody

Annotation of genomic regions:

- TSS: based on a tXDb returns a GRanges with the TSS positions for all transcripts

- distanceFromTSS: based on a GRanges, returnes the GRanges annotated with info about the closer TSS

- GRangesInPromoters: based on a GRanges and a TxDb, subsets the GRanges to those regions overlapping with promoters

- GRmidpoint: returns a GRanges containing the mid point of a GRanges

- GRannotate: based on a GRanges and a TxDb, returns the GRanges with a series of annotations

- GRannotateSimple: a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic

- makeGtfFromDb: utilities to transform a TranscriptDb into a GTF file

Functional annotation:

- enhancers: a GRanges method to define enhancers based on H3K4me1 peaks

- matchEnhancers: a GRanges method to match enhancers with putative targets sites (either TSS or TF-bound TSS)

- topGOres: determines GeneOntology enriched terms for a set of gene ids

- simplifyGOterms: simplify a list of GeneOntology terms based on the list of genes assigned to each GO term

- findLncRNA: identify putative long non coding RNAs (lncRNA) based on ChIP-seq chromatin features and RNAseq data

- getPromoterClass: determining the CpG promoter class and the average CpG content

Visualization:

- heatmapData: Based on a list of GRanges, determine various kind of counts before displaying a heatmap

- palette2d: build a two dimensional color palette

- heatmapPlot: displays the heatmap based on the data from GRheatmapData

- plotStallingIndex: plot the PolII stalling index

Other:

- GR2fasta: A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome

- overlapOfGRanges: given a list of GRanges, all pair-wise overlap are evaluated and the percentage of overlapping ranges is visualized in a heatmap

- GRsetwidth: set the width of a GRanges based on the mid point of each region

- unionMaxScore: GRanges method to perform union of peaks keeping the pvalue of the most significant peak

- GRanges2ucsc: a GRanges method to convert ranges information into UCSC format

- ucsc2GRanges: convert UCSC-formatted genomic positions into a GRanges

### Author(s)

Computational Epigenomics Unit at the Center for Genomic Sciences of IIT@SEMM, Milan, Italy http://genomics.iit.it/groups/computational-epigenomics.html mattia.pelizzola@gmail.com

[Package compEpiTools version 1.24.0 Index]