Convert a data.frame to a GRanges.
Checks that the
data.frame has the required columns,
end, then creates a
GRanges, keeping all of the
## S4 method for signature 'data.frame' annoDF2GR(anno)
Extra columns are added to the
elementMetadata of the
GRanges of the annotation.
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- abcdDNA: A wrapper for fitting the offset-adjusted ABCD-DNA GLM
- absoluteCN: Calculate and Segment Absolute Copy Number from Sequencing...
- AdjustedCopyEstimate-class: Container for results of GC adjusted copy number estimation.
- AffymetrixCdfFile-class: Placeholder For AffymetrixCdfFile Documentation
- AffymetrixCelSet-class: Placeholder For AffymetrixCelSet Documentation
- annoDF2GR: Convert a 'data.frame' to a 'GRanges'.
- annoGR2DF: Convert an annotated 'GRanges' to a 'data.frame'.
- annotationBlocksCounts: Counts the number of sequencing reads within supplied genomic...
- annotationBlocksLookup: Forms a mapping between probe locations and chromosomal...
- annotationCounts: Counts the number of sequencing reads surrounding supplied...
- annotationLookup: Forms a mapping between probes on a tiling array and windows...
- BAM2GRanges: Read in a (list of) BAM file(s) into a GRanges(List) object.
- BayMethList-class: Class '"BayMethList"'
- binPlots: Create line plots of averaged signal across a promoter
- blocksStats: Calculate statistics for regions in the genome
- checkProbes: Check Probe Specificity for Some Regions
- chr21genes: Positions of Genes on Human Chromosome 21
- ChromaBlocks: A function to find areas of enrichment in sequencing data
- ChromaResults-class: ChromaResults class
- chromosomeCNplots: Plot copy number by chromosome
- ClusteredScoresList-class: Container for coverage matrices with clustering results.
- clusterPlots: Visualisation of tables of feature coverages.
- CopyEstimate-class: Container for results of fold change copy number estimation.
- cpgBoxPlots: Boxplots of intensity, binned by Cpg Density
- cpgDensityCalc: Calculate CpG Density in a Window
- cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.
- determineOffset: Function to determine the normalising offset f that accounts...
- empBayes: Function to calculate prior parameters using empirical Bayes.
- enrichmentCalc: Calculate sequencing enrichment
- enrichmentPlot: Plot the distribution of sequencing enrichment.
- expr: Vector of expression differences
- FastQC-class: FastQC and associated classes
- featureBlocks: Make windows for distances around a reference point.
- featureScores: Get scores at regular sample points around genomic features.
- findClusters: Find Clusters Epigenetically Modified Genes
- GCadjustCopy: Calculate Absolute Copy Number from Sequencing Counts
- GCAdjustParams-class: Container for parameters for mappability and GC content...
- GCbiasPlots: Plot GC content vs. Read Counts Before Normalising, and GC...
- gcContentCalc: Calculate The gcContent of a Region
- genomeBlocks: Creates bins across a genome.
- genQC: Plot Quality Checking Information for Sequencing Data
- getProbePositionsDf: Translate Affymetrix probe information in a table.
- getSampleOffsets: Calculates the sample-specific offsets, using the neutral...
- hcRegions: Masking files for hg19
- hyper: Gaussian hypergeometric function for vectorial arguments
- loadPairFile: A routine to read Nimblegen tiling array intensities
- loadSampleDirectory: A routine to read Nimblegen tiling array intensities
- makeWindowLookupTable: Using the output of 'annotationLookup', create a tabular...
- mappabilityCalc: Calculate The Mappability of a Region
- MappabilitySource-class: Superclass for datatypes that can refer to genome mappability...
- maskOut: Function to mask suspicious regions.
- mergeReplicates: Merge GRanges that are of replicate experiments.
- methylEst: Function to derive regional methylation estimates.
- multiHeatmap: Superfigure plots
- plotClusters: Plot Scores of Cluster Regions
- plotQdnaByCN: Plotting the response of qDNA-seq data by CNV
- processNDF: Reads in a Nimblegen microarray design file (NDF)
- profilePlots: Create line plots of averaged signal across a promoter for...
- QdnaData: A container for quantitative DNA sequencing data for ABCD-DNA...
- regionStats: Find Regions of significance in microarray data
- relativeCN: Calculate and Segment Relative Copy Number From Sequencing...
- samplesList: Short Reads from Cancer and Normal
- ScoresList-class: Container for 'featureScores()' output.
- sequenceCalc: Find occurences of a DNA pattern
- setCNVOffsets: Set the CNVOffsets of a 'QdnaData' object
- summarizeScores: Subtract scores of different samples.
- writeWig: Writes sequencing data out into wiggle files