buildAnnotationStore
(Package: recoup) :
Build a local annotation database for recoup
This function creates a local annotation database to be used with recoup so as to avoid long time on the fly annotation downloads and formatting.
● Data Source:
BioConductor
● Keywords:
● Alias: buildAnnotationStore
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calcCoverage
(Package: recoup) :
Calculate coverages over a genomic region
This function returns a coverage list for the genomic regions in mask argument. Generally it should not be used alone and is intended for internal use, although it is useful for calculating stand-alone coverages.
● Data Source:
BioConductor
● Keywords:
● Alias: calcCoverage
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coverageRef
(Package: recoup) :
Calculate coverage in a set of reference genomic
This function fills the coverage field in the main input argument in recoup function.
● Data Source:
BioConductor
● Keywords:
● Alias: coverageRef
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coverageRnaRef
(Package: recoup) :
Calculate coverage in a set of reference genomic
This function fills the coverage field in the main input argument in recoup function.
● Data Source:
BioConductor
● Keywords:
● Alias: coverageRnaRef
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This function connects to the EBI's Biomart service using the package biomaRt and downloads annotation elements (gene co-ordinates, exon co-ordinates, gene identifications, biotypes etc.) for each of the supported organisms. See the help page of recoup for a list of supported organisms. The function downloads annotation for an organism genes or exons. It also uses the UCSC public database connection API to download UCSC and RefSeq annotations.
● Data Source:
BioConductor
● Keywords:
● Alias: getAnnotation
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getBiotypes
(Package: recoup) :
List default Ensembl biotypes
This function returns a character vector of Ensembl biotypes for each supported organism. Mostly for internal use, but can also be used to list the biotypes and use some of them to subset initial genomic regions to be profiled.
● Data Source:
BioConductor
● Keywords:
● Alias: getBiotypes
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kmeansDesign
(Package: recoup) :
Apply k-means clustering to profile data
This function performs k-means clustering on recoup generated profile matrices and stores the result as a factor in the design element. If no design is present, then one is created from the k-means result.
● Data Source:
BioConductor
● Keywords:
● Alias: kmeansDesign
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preprocessRanges
(Package: recoup) :
Read and preprocess BAM/BED files to GRanges
This function reads the BAM/BED files present in the input list object and fills the ranges field of the latter. At the same time it takes care of certain preprocessing steps like normalization.
● Data Source:
BioConductor
● Keywords:
● Alias: preprocessRanges
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profileMatrix
(Package: recoup) :
Calculate final profile matrices for plotting
This function fills the profile field in the main input argument in recoup function by calculating profile matrices from coverages which will be used for plotting.
● Data Source:
BioConductor
● Keywords:
● Alias: profileMatrix
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recoup
(Package: recoup) :
Create genomic signal profiles in predefined or
This function calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The function uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively. The output list object can be reused as input to this function which will automatically recognize which profile elements needto be recalculated, saving time.
● Data Source:
BioConductor
● Keywords:
● Alias: recoup
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