Question: problems in Diffbind In Creating Diffbind Object In R For Chip-Seq Peaks
0
gravatar for xiaoyue.wang
4.3 years ago by
Germany
xiaoyue.wang0 wrote:

Dear All, 

I am trying to input my chip-seq data into diffbind creating diffbind object in R for chip-seq. 

My peaks bed file looks like this

chr1    7088771    7089192    MACS_peak_1    99.81
chr1    7902447    7902565    MACS_peak_2    97.40
chr1    9748281    9748621    MACS_peak_3    163.27

........

I created a sample csv file named "chiptest.csv" like this

SampleID,Peaks

1,1peaks.bed

2,2peaks.bed

When I use 

tbl1=dba(sampleSheet="chiptest.csv")

I keep having error like this,

--------------------------------

1     NA raw

Error in if is.na(peaks)) { : argument is of length zero

----------------------------

Can anyone help me with imporing my own data into diffbind? 

I really would like to use diffbind to analyze my own data. 

Many thanks

Whillie

chip-seq • 2.6k views
ADD COMMENTlink modified 4.2 years ago • written 4.3 years ago by xiaoyue.wang0

Did you check that your peaks.bed file is tab delimited not space delimited?
 

ADD REPLYlink written 4.2 years ago by Ying W3.9k
0
gravatar for xiaoyue.wang
4.2 years ago by
Germany
xiaoyue.wang0 wrote:

thanks for your answer.  I found mistake at bed file where I had only 5 columns, normally there should be 6 or 9 columns. 

Thanks a lot!

Best,

Xiaoyue

ADD COMMENTlink written 4.2 years ago by xiaoyue.wang0
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