diffbind
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ANAMIKA • 0
@ce942b2d
Last seen 15 months ago
India

Enter the body of text here

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
 cell <- dba(sampleSheet = "/home/cytolab/extdata/cell lines data.csv")
1 cal27 ko1 H3K36me2 Treated full media 1 bed
Error in if (file.info(peaks)$size > 0) { : 
  missing value where TRUE/FALSE needed
DiffBind chipseq • 6.3k views
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Hello, please understand that a question without reasonable title, any text and only a malformatted output is not sufficient to diagnose the issue. At least show a selection of the samplesheet and your sessionInfo().

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Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 13 days ago
Cambridge, UK

This error usually indicates that there is some problem with how you have specified the peak files. Is the peak file accessible from the current working directory? Do you have permission to read it?

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yes peak file are accessible from the current working directory and I have the permission to read it

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is there any specific pattern/format of CSV file used as an input ?

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Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 13 days ago
Cambridge, UK

The format of the samplesheet .csv is documented in the help page for dba() for the samplesheet parameter. There are example .csv files included with the package as documented in the examples on that page.

You can test if the files are really accessible as follows:

samples <- read.csv(""/home/cytolab/extdata/cell lines data.csv")
file.access(samples$Peaks)
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