readTranscriptFeatures from genomation
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!
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thymesand •
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Hwaterma •
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Hwaterma •
1 answer
The input for readTranscriptFeatures should be your bed file location.
readTranscriptFeatures("geneannotation.bed")
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