I have a GFF3 file that I turned into a Bed12 file. It load into R and works fine:
>feature_file <- readBed("gene_annotation.bed") Parsed with column specification: cols( X1 = col_character(), X2 = col_double(), X3 = col_double(), X4 = col_character(), X5 = col_double(), X6 = col_character(), X7 = col_double(), X8 = col_double(), X9 = col_double(), X10 = col_double(), X11 = col_number(), X12 = col_character() )
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!