ChIPQC error when running example from documentation
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Entering edit mode
16 months ago
DBScan ▴ 20

I want to use ChIPQC for my own ChIP-Seq samples. I followed to code from the here (example 1, page 3&4): https://bioconductor.org/packages/release/bioc/vignettes/ChIPQC/inst/doc/ChIPQC.pdf

library(ChIPQC)
samples = read.csv(file.path(system.file("extdata", package="ChIPQC"), "example_QCexperiment.csv"))
exampleExp = ChIPQC(samples,annotaiton="hg19")

But I always get this error:

CTCF_1 A549 CTCF   1 bed
Error in if file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed

What am I doing wrong?

ChIP-Seq R ChIPQC • 622 views
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1
Entering edit mode
16 months ago

This occurs when the peak file in question contains no peaks.

From that vignette (see bold):

The actual reads and peak for this experiment are not included with this vignette as they are too large. The sample sheet (see below) include the SRA SRR numbers for each of the experiments, so you can download reads and peaks to fully run the vignette. If you do so, you should put the reads in a sub directory called reads and the peaks in a sub directory called peaks. We intend to make all the vignette data more easily obtainable; email the package authors if you are interested.

So you'll have to download the actual data to run their example.

Your code also has a typo in the annotation parameter spelling:

exampleExp = ChIPQC(samples,annotaiton="hg19")

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I'm an idiot, should have read the tutorial more carefully. The hypo however is also included in the tutorial.

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