Question

window parameter in DataTrack function with a single sample

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rbenel ▴ 40

@rbenel-13642

Last seen 20 months ago

Israel

Hi,

I am trying to understand what input the DataTrack function take from a GRange object. What metadata is included? If there is only a single sample, no grouping needs to be done..

I am wondering because I have only a single sample; however, when I use the parameter window = -1 my plot appears completely different, so I am wondering what exactly is being summarized or averaged?

Code should be placed in three backticks as shown below

#figure out how this works..
dataTrack <- DataTrack(range = peaksGRange, 
                       type = "p", #window = -1, 
                       chromosome = "chr3",
                       start = 169003074 , end = 169005466)

plotTracks(dataTrack)

enter image description here

Gviz • 1.1k views

ADD COMMENT • link 2.6 years ago • updated 2.5 years ago rbenel ▴ 40

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Hi again,

I am still waiting for someone to shed light on this? :)

Thanks

ADD REPLY • link 2.6 years ago rbenel ▴ 40

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Hi,

Can you prepare reproducible example for this? What exactly is the "peaksGRange" object?

Best, Robert

ADD REPLY • link 2.6 years ago Robert Ivanek ▴ 730

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I can provide the BigWigFile here in order to help.

I am mostly interested in the graphics, I would like to produce a smooth histogram of the data...

ADD REPLY • link 2.6 years ago rbenel ▴ 40

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Hi Robert, I think for the most part I figured out some of the issues, but I am still troubled by the yaxis of the DataTrack region...

When plotting together with GeneReionTrack the yaxis is transformed maybe? I can't find any documentation on this.. If you can explain how to change this as a scheme that would be very much appreciated.

Thanks

ADD REPLY • link 2.5 years ago rbenel ▴ 40