Hi Kelly,

no, the suggested code will not work. Yes, you have to provide parameters
for each bam file that you are going to import. In case these parameters
are the same for each of your bam files, this procedure appears to be
redundant. If you want to write more efficient code for such cases you
might want to try something like:

bam.files = "samples.txt" #contains path/file.bam per row for all bam files
that belong to the same group, e.g. biological replicates
bam.files = read.table(bam.files, stringsAsFactors=F)

MSets_groupA = NULL
for(i in 1:nrow(bam.files)){
    MSets_groupA = c(MSets_groupA, MEDIPS.createSet(file=bam.files[i,1],
extend=extend, window_size=window_size, BSgenome=BSgenome, uniq=uniq,
chr.select=chr.select, paired=paired, sample_name=bam.files[i,1]))
    gc()
}

Lukas



On Fri, Dec 20, 2013 at 12:34 PM, Vining, Kelly <
Kelly.Vining@oregonstate.edu> wrote:

>  Hi Lukas,
>
> I have a question about the MEDIPS.createSet function with biological
> replicates. In the vignette, a MEDIPS.createSet command is issued for the
> first replicate of a set, and then other replicates are appended to make a
> list of MEDIPS SETs. Does that mean that one “set” equals one data set from
> one individual, so that I have to have a separate MEDIPS.createSet call
>  for each biological replicate? This seems inefficient, because the
> BSgenome, uniq, extend etc. parameters must be repeated for each rep even
> though all of those parameters are the same across all replicates.
>
>
>
> Can I simply do something like this?
>
>
>
> Rep1_MeDIP = system.file(“extdata”, rep1.bam)
>
> Rep2_MeDIP = system.file(“extdata”, rep2.bam)
>
> Rep3_MeDIP = system.file(“extdata”, rep3.bam)
>
> AllReps = MEDIPS.createSet(c(Rep1_MEDIP, Rep2_MEDIP, Rep3_MEDIP,
> BSgenome=BSgenome)
>
>
>
> Thanks,
>
> --Kelly V.
>
>
>
> *From:* Lukas Chavez [mailto:lukas.chavez.mailings@googlemail.com]
> *Sent:* Wednesday, December 18, 2013 12:42 PM
> *To:* Vining, Kelly
> *Cc:* bioconductor@r-project.org
> *Subject:* Re: [BioC] using custom BSgenome with MEDIPS
>
>
>
>
> Hi Kelly,
>
> let us assume that the package name of your successfully created custom
> BSgenome for e.g. 'oryza sativa' is 'BSgenome.OryzaSativa' and that it is
> installed in your R environment using R CMD INSTALL <package>.
>
> First load your custom BSgenome object into your R session using
>
> library(BSgenome.OryzaSativa)
>
> Note, BSgenome.OryzaSativa will not appear in the list returned by
> available.genomes(). However, in case the library is loaded you should be
> able to immediately use it as usual in MEDIPS like
>
> library(MEDIPS)
> BSgenome=    "BSgenome.OryzaSativa"
>
> MSet = MEDIPS.createSet(file="oryza.bam", BSgenome=BSgenome)
>
> Lukas
>
>
>
>
>
> On Wed, Dec 18, 2013 at 6:57 AM, Vining, Kelly <
> Kelly.Vining@oregonstate.edu> wrote:
>
>
> ________________________________
> From: Vining, Kelly
> Sent: Tuesday, December 17, 2013 10:58 AM
> To: 'Lukas Chavez'
> Cc: bioconductor@r-project.org
> Subject: RE: [BioC] Question about MEDIPS extend parameter
>
> Hello BioC group,
> have created a BSgenome object for my genome of interest, and it is in my
> current working directory. I now want to use it with MEDIPS. How do I make
> it appear under
> >available.genomes()? Is it necessary for my custom genome to appear in
> this list for me to be able to use it with MEDIPS? Or is there a different
> method for accessing this object?
>
> Thanks much,
> --Kelly V.
>
>
>
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>
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>
>

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