topHeatmap: Heatmap and cluster of top variant regions
In imbforge/encodeChIPqc: A set of useful ChIPseq QC metrics from the ENCODE project
Description
Usage
Arguments
Details
Value
Examples
Description
Plot a gplots heatmap with the top variant regions.
Usage
1
topHeatmap(normalizedCounts, ...)
Arguments
normalizedCounts
The normalized data.frame with counts per bin as generated by normalizeTagCount.
...
Extra parameters sent to heatmap.2.
Details
This function uses the heatmap.2 function of gplots to assess
the relationship between samples.
Value
The plotted cluster matrix.
Examples
1
2
3
4
5
6
counts <- tagCount(
samples=c("ctl1.bam", "ctl2.bam", "chip1.bam", "chip2.bam"),
org="Mmusculus", assembly="UCSC", version="mm9"
)
nCounts <- normalizeTagCount(counts)
topHeatmap(nCounts)
imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.
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Description Usage Arguments Details Value Examples
Description
Plot a gplots heatmap with the top variant regions.
Usage
1 | topHeatmap(normalizedCounts, ...)
|
Arguments
normalizedCounts |
The normalized |
... |
Extra parameters sent to |
Details
This function uses the heatmap.2 function of gplots to assess
the relationship between samples.
Value
The plotted cluster matrix.
Examples
1 2 3 4 5 6 | counts <- tagCount(
samples=c("ctl1.bam", "ctl2.bam", "chip1.bam", "chip2.bam"),
org="Mmusculus", assembly="UCSC", version="mm9"
)
nCounts <- normalizeTagCount(counts)
topHeatmap(nCounts)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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