samplesHeatmap: Heatmap and cluster sample-sample distances
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 sample-sample distances.
Usage
1
samplesHeatmap(normalizedCounts, ...)
Arguments
normalizedCounts
The normalized data.frame with counts per bin as generated by normalizeTagCount.
...
Extra params sent to heatmap.2.
Details
This function uses the heatmap.2 function of gplots to assess
the relationship between samples.
Value
The plotted distance 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)
samplesHeatmap(nCounts)
imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.
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.
Description Usage Arguments Details Value Examples
Description
Plot a gplots heatmap with the sample-sample distances.
Usage
1 | samplesHeatmap(normalizedCounts, ...)
|
Arguments
normalizedCounts |
The normalized |
... |
Extra params sent to |
Details
This function uses the heatmap.2 function of gplots to assess
the relationship between samples.
Value
The plotted distance 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)
samplesHeatmap(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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.