[BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS

Sat Dec 21 00:53:42 CET 2013

OK, here's that output:

> BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3"
> library(BSgenome.Ptrichocarpa.Phytozome.v3)
> get(ls(paste("package:",BSgenome, sep="")))
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)
>

________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Matthias Lienhard [lienhard at molgen.mpg.de]
Sent: Friday, December 20, 2013 3:32 PM
To: bioconductor at r-project.org
Subject: Re: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS

OK, that looks alright. What happens when prompting

BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3"
library(BSgenome.Ptrichocarpa.Phytozome.v3)
get(ls(paste("package:",BSgenome, sep="")))

Am 20.12.2013 15:18, schrieb Vining, Kelly:
> Hi Lukas,
> Here's the output:
>
>> BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3"
>> ls("package:BSgenome.Ptrichocarpa.Phytozome.v3")
> [1] "BSgenome.Ptrichocarpa.Phytozome.v3" "Ptrichocarpa"
>> get(ls("package:BSgenome.Ptrichocarpa.Phytozome.v3"))
> 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)
>
> ________________________________
> From: Lukas Chavez [lukas.chavez.mailings at googlemail.com]
> Sent: Friday, December 20, 2013 2:11 PM
> To: Vining, Kelly
> Cc: Lukas Chavez; bioconductor at r-project.org
> Subject: Re: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
>
>
> Hi Kelly,
>
> then there still something does not work with your custom genome.
>
> What is your output for:
>
> library(BSgenome.Ptrichocarpa.Phytozome.v3)
>
> ls("package:BSgenome.Ptrichocarpa.Phytozome.v3")
> get(ls("package:BSgenome.Ptrichocarpa.Phytozome.v3"))
>
> ?
>
> Lukas
>
>
>
>
> On Fri, Dec 20, 2013 at 1:52 PM, Vining, Kelly <Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu>> wrote:
> Hi Lukas,
> I have in my code:
>
>> library(BSgenome.Ptrichocarpa.Phytozome.v3)
>> BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3"
>> budFall2_MEDIP = MEDIPS.createSet(file="accepted_hits_F2.bam", BSgenome=BSgenome, extend=300, uniq=TRUE, shift=0, window_size=1000)
>
> Yes, I am seeing the same error for the first two .bam files I submitted, so figured I'd better stop until I figured out what was going on.
>
> --Kelly
>
>
> From: Lukas Chavez [mailto:lukas.chavez at googlemail.com<mailto:lukas.chavez at googlemail.com>]
> Sent: Friday, December 20, 2013 1:42 PM
> To: Vining, Kelly
> Cc: Lukas Chavez; bioconductor at r-project.org<mailto:bioconductor at r-project.org>
> Subject: Re: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
>
> Hi Kelly,
> No, youshould not ignore the error message. I did not fully understand, if this happens for all of your bam files or only for one of your bam files? What do you have on your BSgenome variable, I cannot see this in your code?
> Lukas
>
> On Fri, Dec 20, 2013 at 1:00 PM, Vining, Kelly <Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu><mailto:Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu>>> wrote:
> A follow-up question about an error message with MEDIPS.createSet command: when I load my reference genome, the create a MEDIPS set with one of my .bam files, I get the following error message:
>
>> library(BSgenome.Ptrichocarpa.Phytozome.v3)
>> budFall2_MEDIP = MEDIPS.createSet(file="accepted_hits_F2.bam", BSgenome=BSgenome, extend=300, uniq=TRUE, shift=0, window_size=1000)
> Reading bam alignment accepted_hits_F2.bam
> Total number of imported short reads: 46734466
> Extending reads...
> Creating GRange Object...
> Extract unique regions...
> Number of unique short reads: 36603869
> Error in as.environment(pos) :
>    no item called "paste("package:", BSgenome, sep = "")" on the search list
> In addition: Warning message:
> In ls(paste("package:", BSgenome, sep = "")) :
>    àpaste("package:", BSgenome, sep = "")à converted to character string
>
> I don't know how to interpret this. Is this error generated from GenomicRanges? Does it indicate that I've done something incorrectly, or is it safe to ignore it?
>
> Thanks again,
> --Kelly V.
> ________________________________________
> From: bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org><mailto:bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org>> [bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org><mailto:bioconductor-bounces at r-project.org<mailto:bioconductor-bounces at r-project.org>>] on behalf of Vining, Kelly [Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu><mailto:Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu>>]
> Sent: Friday, December 20, 2013 12:34 PM
> To: 'Lukas Chavez'
> Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org><mailto:bioconductor at r-project.org<mailto:bioconductor at r-project.org>>
> Subject: [BioC] separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
>
> 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 at googlemail.com<mailto:lukas.chavez.mailings at googlemail.com><mailto:lukas.chavez.mailings at googlemail.com<mailto:lukas.chavez.mailings at googlemail.com>>]
> Sent: Wednesday, December 18, 2013 12:42 PM
> To: Vining, Kelly
> Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org><mailto:bioconductor at r-project.org<mailto:bioconductor at 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 at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu><mailto:Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu>><mailto:Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu><mailto:Kelly.Vining at oregonstate.edu<mailto:Kelly.Vining at oregonstate.edu>>>> wrote:
>
> ________________________________
> From: Vining, Kelly
> Sent: Tuesday, December 17, 2013 10:58 AM
> To: 'Lukas Chavez'
> Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org><mailto:bioconductor at r-project.org<mailto:bioconductor at r-project.org>><mailto:bioconductor at r-project.org<mailto:bioconductor at r-project.org><mailto:bioconductor at r-project.org<mailto:bioconductor at 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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