error when create dba object
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@xieyongjun93-13638
Last seen 6.8 years ago

Hi!

    When I use the function dba to create a dba object, I always encounter the error : 

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

my code is :

a <- dba(sampleSheet = 'samplesheet.csv')

and the samplesheet.csv is as follows :

SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
zh11_drought_01 leaf TF drought water 1 zh11_drought_01_filter.bam zh11_drought_input_01 zh11_drought_input_01_filter.bam zh11_drought_01_peaks.xls macs
zh11_drought_02 leaf TF drought water 2 zh11_drought_02_filter.bam zh11_drought_input_02 zh11_drought_input_02_filter.bam zh11_drought_02_peaks.xls macs
zh11_drought_03 leaf TF drought water 3 zh11_drought_03_filter.bam zh11_drought_input_03 zh11_drought_input_03_filter.bam zh11_drought_03_peaks.xls macs
zh11_normal_01 leaf TF normal water 1 zh11_normal_01_filter.bam zh11_normal_input_01 zh11_normal_input_01_filter.bam zh11_normal_02_peaks.xls macs
zh11_normal_02 leaf TF normal water 2 zh11_normal_02_filter.bam zh11_normal_input_02 zh11_normal_input_02_filter.bam zh11_normal_03_peaks.xls macs
zh11_normal_03 leaf TF normal water 3 zh11_normal_03_filter.bam zh11_normal_input_03 zh11_normal_input_03_filter.bam zh11_normal_04_peaks.xls macs

the peaks files are calculated by macs2.

Can someone give me some advices? Many thanks!

diffbind • 1.1k views
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Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 5 weeks ago
Cambridge, UK

This error is saying that there is an issue accessing one or more of the Peaks file(s). You can run file.info() on the Peaks files, eg

file.info("zh11_drought_01_peaks.xls")

For each peak file, to make sure they are all there with read access and actual data inside.

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