Question: Diffbind bioconductor, peaks overlapping
0
gravatar for marina-orlova
4.5 years ago by
Russian Federation
marina-orlova70 wrote:

Hello

Can you please help me with diffbind package.

As I understood I should create a csv file with names of bed files with input, control and peaks bed files of peaksets.

Are all of these files required for analysis? Can I do only with files with peaks? I'm trying to do without initial files (just don't have them) writing a csv file as follows:

SampleID,Peaks
1,2A.peaks.bed
2,3A.peaks.bed
3,5A.peaks.bed

But using this in R I have a mistake:

> sets = dba(sampleSheet="sample.csv")
1     NA raw
Error in Summary.factor(c(1L, 1112L, 2223L, 3334L, 4445L, 5556L, 6592L,  : 
  max not meaningful for factors
Warning:
In read.table(samplesheet, sep = ",", stringsAsFactors = F, header = T) :
  incomplete final line found by readTableHeader on 'sample.csv'

 

 

diffbind chip-seq bioconductor • 3.3k views
ADD COMMENTlink written 4.5 years ago by marina-orlova70
1

Hi Marina,

I was facing similar problem. I think, unknowingly you got some spaces  while writing the CSV file. Open the file in a texteditor (e.g Textedit for MAC or Notepad for Windows) and then check if there are any unwanted spaces.

The file should somewhat look like this

SampleID,XXX,YYY,AAA

Not like this

SampleID,XXX, YYY,AAA 

Even check the end of a line to see any extra spaces, which is visually unrecognizable

Thanks

ADD REPLYlink written 4.5 years ago by nirmalyasaha200310

Hi, thank you for the reply, I managed to make it work )

ADD REPLYlink written 4.4 years ago by marina-orlova70

Hi Marina-orlova, May you please tell how you made it work? I met the same problem now. Thanks.

ADD REPLYlink written 3.9 years ago by zwang06140

Hi zwang,

You need to make sure that your peak file is formatted correctly. It must be in BED format and follow this form:

CHROMOSOME   START   END   SCORE

ADD REPLYlink written 3.5 years ago by Jens Lichtenberg0
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