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