readTranscriptFeatures from genomation

Question

[Hwaterma]

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!

[lieven.sterck]

A small educational note: I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Answer 1

[thymesand]

The input for readTranscriptFeatures should be your bed file location. readTranscriptFeatures("geneannotation.bed")