Data Smoothing - Matlab
0
0
Entering edit mode
9.2 years ago
timjoncooper ▴ 310

Hi,

I'm attempting to smooth genome-wide data that is currently in a bedGraph format in an attempt to remove problems visualising the data which is skewed toward single 1bp peaks with high signal amongst regions of low signal - such as the one highlighted below:

chrI 86 87 1

chrI 108 109 1

chrI 297 298 1

chrI 395 396 1

chrI 399 400 1

chrI 411 412 455

chrI 413 414 1

chrI 414 415 1

chrI 416 417 2

Within MatLab i've carried out smoothing by using a Hann window, creating it with:

hann15=hanning(15);

and smoothing the signal with:

smooth15=conv(signal,hann15,'same');

However i've noticed that if I manually alter signal data to include an aberrantly strong peak of the kind we are trying to reduce the prevalence of - this smoothing method includes the new value and constructs a smoothed peak bias toward this one outlier.

Is there a way to get around this? Perhaps I need a new smoothing window shape?

Thanks for any help!

  • TJC
matlab data • 2.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 1307 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6