[BioC] MEDIPS.createSet error

[Steve Lianoglou]

Hi,

Caveat being that I've never used MEDIPS, and I'm just going along with 
the vignette.

So, comments inline:


On 31 Mar 2014, at 13:09, Vining, Kelly wrote:

> Hi,
> Thanks for the advice thus far! To confirm what is in my BSgenome 
> variable, I did this:
>
>> class(BSgenome)
> [1] "BSgenome"
> attr(,"package")
> [1] "BSgenome"
>> names(BSgenome)
> [1] "Chr01" "Chr02" "Chr03" "Chr04" "Chr05" "Chr06" "Chr07" "Chr08" 
> "Chr09"
> [10] "Chr10" "Chr11" "Chr12" "Chr13" "Chr14" "Chr15" "Chr16" "Chr17" 
> "Chr18"
> [19] "Chr19" "scaf"
>
> And then:
>> print(BSgenome)
> Black cottonwood genome
> |
> | organism: Populus trichocarpa (Black cottonwood)
> | provider: Phytozome (JGI)
> | provider version: 3.0
> | release date: January 2010
> | release name: Populus trichocarpa v3.0
> |
> | single sequences (see '?seqnames'):
> |   Chr01  Chr02  Chr03  Chr04  Chr05  Chr06  Chr07  Chr08  Chr09  
> Chr10  Chr11
> |   Chr12  Chr13  Chr14  Chr15  Chr16  Chr17  Chr18  Chr19
> |
> | multiple sequences (see '?mseqnames'):
> |   scaf
> |
> | (use the '$' or '[[' operator to access a given sequence)
>
>
> So that looks ok. Interestingly, when I followed the vignette and did 
> the equivalent of
> BSgenome="BSgenome.Hsapiens.UCSC.hg19"

The vignette suggests that BSgenome should be the package name of the 
BSgenome package to open, so yours should be something like 
"BSgenome.Ptrichocarpa.XXX.YY" or something -- I guess you built this 
packge by yourself, or something, so you'd know its name ...

> That didn't work for me. It only worked without quotes. If I included 
> quotes, it just assigned a character vector to that variable.

Sorry, what exactly didn't work for you? Can you show me the code that 
failed?

> Then, following your advice:
>
>> si.bsg <- seqinfo(BSgenome.Ptrichocarpa.Phytozome.v3)
>> si.bam <- seqinfo(BamFile("FallBud_brep1_aln_sorted.bam"))
> Error in seqinfo(BamFile("FallBud_brep1_aln_sorted.bam")) :
> error in evaluating the argument 'x' in selecting a method for 
> function 'seqinfo': Error: could not find function "BamFile"

The BamFile function is defined in the Rsamtools package, you need to 
load that first (the first line of code I suggested you run was to load 
the Rsamtools package). Load it first, then redo the 
seqinfo(BamFile(...)) stuff.

-steve