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
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.
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