DiffBind: error with dba.peakset()
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hkitano • 0
@hkitano-23077
Last seen 4.7 years ago

I'm trying to load in peaksets from a BED file (the summits output from macs2 callpeaks), and I'm running into an error

Here's what the first line of my BED file looks like:

chr1    4785666 4785667 BMDM-RNAPIIpS2-CTR-1-ChIPseq-GTACACCT_S9_L003_R1_001_peak_1 18.38304

And my DiffBind call us

ctr <- dba.peakset(NULL, 
               peaks="BMDM-RNAPIIpS2-CTR-1-ChIPseq-GTACACCT_S9_L003_R1_001_summits.bed",
               peak.caller="bed",
               sampID="CTR-1",
               replicate=1)

My error reads "Error in if file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed"

What is the issue? I'm new to DiffBind so I'm not sure what's going on. Thank you!

DiffBind Peakset • 756 views
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sorry, my working directory was wrong!

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Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 4 weeks ago
Cambridge, UK

You probably shouldn't be using the *_summits.bed files, which identify only the point of maximal pileup, but rather the *_peaks.xls files, which include the full enriched intervals.

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