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CoverageView (version 1.8.0)

Coverage visualization package for R

Description

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome

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Version

Version

1.8.0

License

Artistic-2.0

Maintainer

Ernesto Lowy

Last Published

February 15th, 2017

Functions in CoverageView (1.8.0)

export.wig

Generates a WIG file containing the coverage values for a certain genomic interval
DF_H3K36me3

Example of a coverage matrix using the ChIP-seq data for the H3K36me3 histone modification experiment
genome.covplot.depth

Generates a genome coverage plot
DF_H3K4me3_nopeaks_ratios

Example of a matrix with the ratio of the coverages using the ChIP-seq data for the H3K4me3 histone modification experiment
FoxA1_chr19

Example of a coverage matrix using the ChIP-seq data for the FoxA1 transcription factor experiment
cov.matrix

Compute a coverage matrix
write.profile

Write coverage values into a file
DF_H3K4me3_ctl

Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K4me3 histone modification experiment
CoverageView-internal

Internal Methods
draw.profile

Draw a coverage profile
genome.covplot.cumdepth

Generates a cumulative genome coverage plot
CoverageView-package

Coverage visualization package for R
DF_H3K4me3

Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experiment
CoverageBigWigFile-class

Class "CoverageBigWigFile"
DF_H3K36me3_control

Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K36me3 histone modification experiment
draw.heatmap

Draw a coverage heatmap
cov.interval

arithmetic operation on an interval
CoverageBamFile-class

Class "CoverageBamFile"