genomation readTrancriptFeature error reading UCSC bed

[eguevara]

Hi all,

I would like to annotate DM CpGs. But I am getting stuck on the very first step trying to import my annotations and so am hoping someone here will be able to offer some guidance!

I followed the instructions to download a bed file of RefSeq genes for my species and assembly (panTro4) (attached here). However, when I try to import the file using this command:

gene.obj=readTranscriptFeatures(system.file("extdata","panTro4-RefSeqGenes.bed.txt", package = "methylKit"))

I get the following error:

Reading the table...

Error in read.table(file = filename, sep = sep, skip = skip, nrows = 30,  : 

  no lines available in input

In addition: Warning messages:

1: In file(filename, open = "r") :

  file("") only supports open = "w+" and open = "w+b": using the former

2: In file(file, "rt") :

  file("") only supports open = "w+" and open = "w+b": using the former

I've googled around on the contents of the error and it seems like it could be to do with how the file is called or permissions, but haven't been able to find a solution. I see there have been plenty of errors reported here resulting from converted files, but this was downloaded straight from UCSC. I've tried simplifying the number of fields from what is output by default by the Table Browser, but that doesn't help.

If anyone has any suggestions, they would be greatly appreciated! Or, if I am making a rookie mistake or missing something obvious, my apologies in advance! Or it may be more appropriate to direct this to the genomation community specifically, but figured I would give it a shot here.

Cheers,

Elaine

[Altuna Akalin]

gene.obj=readTranscriptFeatures(system.file("extdata","panTro4-RefSeqGenes.bed.txt", package = "methylKit"))

why are you using system.file(), did you put the file in the installed directory of the package ?

 

I get the following error:

Reading the table...

Error in read.table(file = filename, sep = sep, skip = skip, nrows = 30,  : 

  no lines available in input

In addition: Warning messages:

1: In file(filename, open = "r") :

  file("") only supports open = "w+" and open = "w+b": using the former

2: In file(file, "rt") :

  file("") only supports open = "w+" and open = "w+b": using the former

I've googled around on the contents of the error and it seems like it could be to do with how the file is called or permissions, but haven't been able to find a solution. I see there have been plenty of errors reported here resulting from converted files, but this was downloaded straight from UCSC. I've tried simplifying the number of fields from what is output by default by the Table Browser, but that doesn't help.

If anyone has any suggestions, they would be greatly appreciated! Or, if I am making a rookie mistake or missing something obvious, my apologies in advance! Or it may be more appropriate to direct this to the genomation community specifically, but figured I would give it a shot here.

Cheers,

Elaine

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[eguevara]

Hi Altuna,

Thanks for the reply!

I used system.file () because I was following (clearly too literally!! and without enough thought) this vignette using the example data.

I did try using file() and read.table() in lieu of system.file(), as it did seem to me like that could be the problem, but those also gave errors. But I did not think try using simply (embarrassingly obvious now!):

gene.obj=readTranscriptFeatures("panTro4-RefSeqGenes.bed.txt")

which works beautifully, just as it should. Thanks again for your help pointing out where I was going wrong.

Cheers,

Elaine