problems in Diffbind In Creating Diffbind Object In R For Chip-Seq Peaks

Question

[xiaoyue.wang]

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

[Ying W]

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

[xiaoyue.wang]

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