[BioC] MEDIPS.createSet error
lianoglou.steve at gene.com
Mon Mar 31 22:15:30 CEST 2014
Caveat being that I've never used MEDIPS, and I'm just going along with
So, comments inline:
On 31 Mar 2014, at 13:09, Vining, Kelly wrote:
> Thanks for the advice thus far! To confirm what is in my BSgenome
> variable, I did this:
>  "BSgenome"
>  "BSgenome"
>  "Chr01" "Chr02" "Chr03" "Chr04" "Chr05" "Chr06" "Chr07" "Chr08"
>  "Chr10" "Chr11" "Chr12" "Chr13" "Chr14" "Chr15" "Chr16" "Chr17"
>  "Chr19" "scaf"
> And then:
> 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
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
> 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
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