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!

The error might be a bit obscure, so here's a translation: it's saying that the first argument to readTranscriptFeatures is supposed to be something other than a GRanges object. Which you could have known if you read the help file (which is what you should have done first!).

Description:

     Function for reading exon intron and promoter structure from a
     given bed file

Usage:

     readTranscriptFeatures(location,remove.unusual=TRUE,
                                   up.flank=1000,down.flank=1000,unique.prom=TRUE)

     ## S4 method for signature 'character'
     readTranscriptFeatures(location, remove.unusual = TRUE,
       up.flank = 1000, down.flank = 1000, unique.prom = TRUE)

Arguments:

location: location of the bed file with 12 or more columns.  The file
          can end in .gz, .bz2, .xz, or .zip and/or start with
          http:// or ftp://. If the file is not compressed it can
          also start with https:// or ftps://.

Which seems to clearly outline what you are supposed to be doing?

GFF to bed12 conversion doesn’t always work. Assuming it worked, you should just use provide the bed12 file path as the first argument to readTranscriptFeatures function

Best

Altuna

Sent from mobile, excuse the brevity