Question: readTranscriptFeatures from genomation
0
gravatar for Hwaterma
24 days ago by
Hwaterma0
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
1

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:

101010 Button

ADD REPLYlink written 24 days ago by lieven.sterck6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 985 users visited in the last hour