Deeptools, ComputeMatrix and plotProfile

Question

[Ar Es]

Hi all,

I have a question about ComputeMatrix and plotProfile from deeptools. I have a compute matrix output for 5 samples and I'd like to generate a signal plot (only one line), that represents average value (rowMeans for each region) across all samples but I couldn't find it in the plotProfile functions.

What I got was an average plot for each samples on one single plot which was not what I wanted. here is my code:

 plotProfile --matrixFile input.matrix.gz --outFileName Average.plot.pdf --dpi 300 --averageType mean --colors orange --plotTitle 'Ave plot'

Could you please help me out with this issue? I tried to manipulate the output in R but the matrix is huge and my computer cannot handle it.

Thank you, AR

Answer 1

[Devon Ryan]

You would need to merge the samples together, since we otherwise always assume that users want to keep samples separate so they can assess variance. So either sum/average the bigWigs with wiggletools or use computeMatrix operations to firstly slice and then rbind the samples so the appear as a single sample.

[Ar Es]

I understood the rbind part from ComputeMatrixOperation but I didn't get what do you mean by slice? do you mean subsetting the matrix by samples and then rbind them all together? Thanks.

[Devon Ryan]

Yeah, exactly that