Question: readTranscriptFeatures from genomation
gravatar for Hwaterma
24 days ago by
Hwaterma0 wrote:

I have a GFF3 file that I turned into a Bed12 file. It load into R and works fine:

featurefile <- readBed("geneannotation.bed")

Parsed with column specification:

cols( X1 = colcharacter(),X2 = coldouble(), X3 = coldouble(), X4 = colcharacter(), X5 = coldouble(), X6 = colcharacter(), X7 = coldouble(), X8 = coldouble(), X9 = coldouble(), X10 = coldouble(), X11 = colnumber(), X12 = colcharacter() )

Then I try to run readTranscriptFeatures and I keep getting this error:

features <- readTranscriptFeatures(feature_file, up.flank=1001, down.flank=0, unique.prom=FALSE, remove.unusual=FALSE)

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘readTranscriptFeatures’ for signature ‘"GRanges"’

I am not sure what this means or how to fix it. Please help!

ADD COMMENTlink modified 24 days ago by lieven.sterck6.4k • written 24 days ago by Hwaterma0

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ADD REPLYlink written 24 days ago by lieven.sterck6.4k
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