Coverage visualization package for R


[Up] [Top]

Documentation for package ‘CoverageView’ version 1.0.0

Help Pages

CoverageView-package Coverage visualization package for R
cov.interval arithmetic operation on an interval
cov.interval-method arithmetic operation on an interval
cov.matrix Compute a coverage matrix
cov.matrix-method Compute a coverage matrix
CoverageBamFile Class '"CoverageBamFile"'
CoverageBamFile-class Class '"CoverageBamFile"'
CoverageBigWigFile Class '"CoverageBigWigFile"'
CoverageBigWigFile-class Class '"CoverageBigWigFile"'
CoverageView Coverage visualization package for R
DF_H3K36me3 Example of a coverage matrix using the ChIP-seq data for the H3K36me3 histone modification experiment
DF_H3K36me3_control Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K36me3 histone modification experiment
DF_H3K4me3 Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experiment
DF_H3K4me3_ctl Example of a coverage matrix using the control replicate for the ChIP-seq data for the H3K4me3 histone modification experiment
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
draw.heatmap Draw a coverage heatmap
draw.heatmap-method Draw a coverage heatmap
draw.profile Draw a coverage profile
draw.profile-method Draw a coverage profile
export.wig Generates a WIG file containing the coverage values for a certain genomic interval
export.wig-method Generates a WIG file containing the coverage values for a certain genomic interval
FoxA1_chr19 Example of a coverage matrix using the ChIP-seq data for the FoxA1 transcription factor experiment
genome.covplot.cumdepth Generates a cumulative genome coverage plot
genome.covplot.cumdepth-method Generates a cumulative genome coverage plot
genome.covplot.depth Generates a genome coverage plot
genome.covplot.depth-method Generates a genome coverage plot
path-method Class '"CoverageBamFile"'
reads_mapped-method Class '"CoverageBamFile"'
run_type-method Class '"CoverageBamFile"'
show-method Class '"CoverageBamFile"'
show-method Class '"CoverageBigWigFile"'
write.profile Write coverage values into a file
write.profile-method Write coverage values into a file