I am using ChIPQC to get quality metrics of my reads. I have .bam files and .narrowpeaks files. I created a sample csv file called sample1.csv. The sample.csv sheet can be found at this link.
My code is the following:
> samples <- read.csv('sample1.csv')
> View(samples)
> chipObj <- ChIPQC(samples, annotation="hg38")
However, I keep getting this error:
Error in if file.info(peaks)$size > 0) { :
missing value where TRUE/FALSE needed
Hope someone can help. I really would appreciate it.
3 answers
I figured it out. The peak files I had generated needed to have the prefix "chr" before the chromosome number. So before it would be just 1, 2,3,......,X,Y. After the change it is chr 1, chr 2, chr 3............ chr X, chr Y. Thanks for all your help guys. If anyone is having a similar issue please message me, would love to help out.
One of your peaks files contains no peaks, potentially due to poor ChIP enrichment or other issues with peakcalling.
It would help to see your sample sheet sample1.csv.
The most common source of this error is the format of the peaks files not matching what is specified in the PeakCaller column. What is the type of the peak files, and what is specified in the sample sheet?
Thank you for answering, my sample.csv link is below, you should be able to access it: I appreciate your help in this very much.
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ChIP QC
written by mropri
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ChIPQC showed errors 'nnodes' must be >= 1
written by lkw.wang •
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