topHeatmap: Heatmap and cluster of top variant regions

Description Usage Arguments Details Value Examples

View source: R/binned_pca.R

Description

Plot a gplots heatmap with the top variant regions.

Usage

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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

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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.