R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
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Results 1 - 10 of 12 found.
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CoverageBamFile-class (Package: CoverageView) : Class code{"CoverageBamFile"

The CoverageBamFile class contains information on a BAM file and inherits fields from the BamFile class in the Rsamtools package.

● Data Source: BioConductor
● Keywords: classes
● Alias: CoverageBamFile, CoverageBamFile-class
● 0 images

CoverageBigWigFile-class (Package: CoverageView) : Class code{"CoverageBigWigFile"

The CoverageBigWigFile class contains information on a BigWIG file and inherits fields from the BigWigFile class in the rtracklayer package.

● Data Source: BioConductor
● Keywords:
● Alias: CoverageBigWigFile, CoverageBigWigFile-class
● 0 images

CoverageView-internal (Package: CoverageView) : Internal Methods

Internal CoverageView functions

● Data Source: BioConductor
● Keywords: internal
● Alias: .bed.to.GRanges, .cov.bin, .do.normalization, .gff.to.GRanges, CoverageView-internal, cov.bin, cov.bin,ANY,missing,numeric,GRanges,missing-method, cov.bin,ANY,missing,numeric,missing,CoverageBamFile,missing-method, cov.bin,ANY,missing,numeric,missing,CoverageBigWigFile,missing-method, cov.bin,ANY,missing,numeric,missing,missing-method, cov.bin,ANY,numeric,missing,GRanges,missing-method, cov.bin,ANY,numeric,missing,missing,CoverageBamFile,missing-method, cov.bin,ANY,numeric,missing,missing,CoverageBigWigFile,missing-method, cov.bin,ANY,numeric,missing,missing,missing-method, cov.bin,missing,missing,missing,GRanges,character-method, cov.bin,missing,missing,missing,GRanges,missing,character-method, cov.bin,missing,missing,missing,missing,CoverageBamFile,character-method, cov.bin,missing,missing,missing,missing,character-method, cov.bin-methods, imageScale
● 0 images

CoverageView-package (Package: CoverageView) :

Package for the generation of coverage profiles using data originated in different types of NGS experiments

● Data Source: BioConductor
● Keywords:
● Alias: CoverageView, CoverageView-package
● 0 images

cov.interval (Package: CoverageView) : arithmetic operation on an interval

This method computes a numeric vector with the result of a certain arithmetic operation with the coverage for two particular BAM or BigWIG files within a specific genomic interval defined by the user

● Data Source: BioConductor
● Keywords:
● Alias: cov.interval, cov.interval,CoverageBamFile,CoverageBamFile-method, cov.interval,CoverageBamFile-method, cov.interval,CoverageBigWigFile,CoverageBigWigFile-method, cov.interval,CoverageBigWigFile-method
● 0 images

cov.matrix (Package: CoverageView) : Compute a coverage matrix

This method generates a coverage matrix for which each column is a different genomic feature (i.e. the coordinate of the transcription start site) or genomic interval (defined by start/end coordinates) and each row can be either a position or a bin related to this feature or interval. Each element in the matrix is the result of computing the coverage value for this position/bin that is at a certain distance upstream or dowstream the genomic feature (i.e. the TSS) or it is in the genomic interval

● Data Source: BioConductor
● Keywords:
● Alias: cov.matrix, cov.matrix,ANY,ANY-method, cov.matrix,ANY,missing-method
● 0 images

draw.heatmap (Package: CoverageView) : Draw a coverage heatmap

This method draws a heatmap of the coverage values using the matrix that is passed as an argument to the method

● Data Source: BioConductor
● Keywords:
● Alias: draw.heatmap, draw.heatmap,list-method, draw.heatmap,matrix-method
● 0 images

draw.profile (Package: CoverageView) : Draw a coverage profile

This method draws a coverage profile for the coverage matrix that is passed as an argument to the method

● Data Source: BioConductor
● Keywords:
● Alias: draw.profile, draw.profile,list-method, draw.profile,matrix-method
● 0 images

export.wig (Package: CoverageView) : Generates a WIG file containing the coverage values for a certain genomic interval

Write the coverage values calculated using the cov.interval function into a WIG format file

● Data Source: BioConductor
● Keywords:
● Alias: export.wig, export.wig,numeric-method
● 0 images

genome.covplot.cumdepth (Package: CoverageView) : Generates a cumulative genome coverage plot

This method generates a plot showing the percentage of the genome covered at different read depths

● Data Source: BioConductor
● Keywords:
● Alias: genome.covplot.cumdepth, genome.covplot.cumdepth,CoverageBamFile-method, genome.covplot.cumdepth,list-method
● 0 images