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I encountered an error while using R Diffbind for data analysis

I'm now trying to use R Diffbind for differential peak analysis, and encountered the following problem:

> HBV<-dba(sampleSheet = "/data6/sample_inf.csv")
Core_1  HBV  Core 1 bed
Core_2  HBV  Core 2 bed
TP_1  HBV  TP 1 bed
TP_2  HBV  TP 2 bed
Error in if (sum(res$peaks[[1]]$Score < 0) > 0) { : 
  missing value where TRUE/FALSE needed

The sampleSheet is as follows.

> sample_inf
  SampleID Factor Replicates Treatment                                                       bamReads
1   Core_1    HBV          1      Core /data6/H3K4me_bigwig/Core-H3K4me-1_Shift.dedual.sorted.bam
2   Core_2    HBV          2      Core /data6/H3K4me_bigwig/Core-H3K4me-2_Shift.dedual.sorted.bam
3     TP_1    HBV          1        TP   /data6/H3K4me_bigwig/Tp-H3K4me-1_Shift.dedual.sorted.bam
4     TP_2    HBV          2        TP   /data6/H3K4me_bigwig/Tp-H3K4me-2_Shift.dedual.sorted.bam
                                                   Peaks PeakCaller
1 /data6/H3K4me_bigwig/Core-H3K4me-1.clean.clean.bed        bed
2 /data6/H3K4me_bigwig/Core-H3K4me-2.clean.clean.bed        bed
3   /data6/H3K4me_bigwig/Tp-H3K4me-1.clean.clean.bed        bed
4   /data6/H3K4me_bigwig/Tp-H3K4me-2.clean.clean.bed        bed
diffbind r
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written by Pallondyle • Pallondyle

The error itself means that this snipped, supposed to check whether any peak has score below zero, neither receives TRUE or FALSE but something like NA. Not helpful for you (or me). What it could mean is that there is a problem with the peak files. Is one of the bed files empty or malformatted?

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written by ATpoint ATpoint

I reassigned the score in all peak files to the value of 1000, and then the code can run. I called peak from the.Bdg file. Maybe it is for this reason that there is a problem with the value of that column.

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written by Pallondyle • Pallondyle

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