Have no function 'bedToGR'

[MuradOmarov]

Hi! Thanks for your great tool! I'm trying to use ORFik to analyze uORFs. And I want to find them in regions between start sites of assembled transcripts and annotated CDS start sites. So I want to add this regions from Bed-file b =read.table('UTRs.bed') bedToGR(b) Error in bedToGR(b) : could not find function "bedToGR"

My console output during installation:

Bioconductor version 3.14 (BiocManager 1.30.15), R 4.1.0 (2021-05-18) Installing package(s) 'ORFik' trying URL 'http://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/ORFik_1.13.2.tgz' Content type 'application/x-gzip' length 4250572 bytes (4.1 MB)

downloaded 4.1 MB

tar: Failed to set default locale

The downloaded binary packages are in /var/folders/_k/nmqkfdns21752hfl4205tzgw0000gp/T//RtmpKEqFge/downloaded_packages Warning message: In .inet_warning(msg) : unable to access index for repository http://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1: cannot open URL 'http://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES'

Thanks in advance!

[Roleren]

hehe, yeah, this function is only for internal use, and is not exported (AKA, another function is what you should use):

if you try:

library(ORFik)
fread.bed('UTRs.bed') # This uses fread, so much faster than read.table

I even have a function that loads any file type:

fimport('UTRs.bed') # Works for bed, bam, wig, ofst, ++

You should not use internal functions. But if you wanted to, you would have to do:

b <- read.table('UTRs.bed')
ORFik:::bedToGR(b) # To access internal functions use 3 :::

Let me know if you have more questions.

[MuradOmarov]

Got you! Thanks! It works