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rinnlab / BrainMap

Mouse lncRNA Brain Map Project Data and Analysis
http://www.pnas.org/content/112/22/6855.abstract
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occasional track errors (linc-cox2 adult, embryonic, and haunt adult) #7

Open agroff11 opened 10 years ago

agroff11 commented 10 years ago

Linc-Cox2 adult and embryonic, and haunt embryonic have issues with gene tracking. I though the cummerbund method would fix this but it doesnt.

In .md output, error is: ## Error: dims [product 3] do not match the length of object [4]

And when I work back through I find that everything works (with the cummerbund makeGeneTrack method) until plotTracks, where I get "Error in n - 1 : non-numeric argument to binary operator"

traceback() 12: movingAverage(x, window) at #3 11: trans(vals) 10: .local(x, ...) 9: score(GdObject) 8: score(GdObject) 7: .local(GdObject, ...) 6: collapseTrack(GdObject, diff = diff, xrange = c(minBase, maxBase)) 5: collapseTrack(GdObject, diff = diff, xrange = c(minBase, maxBase)) 4: .local(GdObject, ...) 3: drawGD(trackList[[i]], minBase = ranges["from"], maxBase = ranges["to"], prepare = TRUE, subset = FALSE) 2: drawGD(trackList[[i]], minBase = ranges["from"], maxBase = ranges["to"], prepare = TRUE, subset = FALSE) 1: plotTracks(myTracks, from = from, to = to, chromosome = myChr, showAxis = FALSE, background.title = "black", col.title = "white", col.axis = "black", sizes = trackSizes, geneSymbol = TRUE)

I'm not entirely sure what's going on with these 3. Haunt adult works fine (and an iteration or two ago, so did cox2 embryonic)

thoughts?!

Loyale commented 10 years ago

Looks like the problem is with my movingAverage() function. Can you adjust the window size or don't do a transform for those particular genes?