Indeed, that also looks fine. Then, unfortunately, I do not have a clue what's going on. What happens in the MEDIPS.createSet function is the following: (...) dataset=get(ls(paste("package:", BSgenome, sep=""))) chr_lengths=as.numeric(seqlengths(dataset)[chromosomes]) (...) where 'chromosomes' has been pre-calculated based on the set of chromosomes in your bam files and/or by the chr.select parameter. You could try if the following works: library(BSgenome.Ptrichocarpa.Phytozome.v3) BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3" dataset=get(ls(paste("package:", BSgenome, sep=""))) chromosomes=c("Chr01", "Chr02") chr_lengths=as.numeric(sapply(chromosomes, function(x){as.numeric(length(dataset[[x]]))})) If this works (i.e. you have the sizes of the chromosomes "Chr01", "Chr02" at "chr_lengths"), then I do not see why there will be an error in MEDIPS. Can you send the whole script you execute up to the MEDIPS.createSet function that causes the error? Lukas On Fri, Dec 20, 2013 at 4:01 PM, Matthias Lienhard <lienhard@molgen.mpg.de>wrote: > Now I' stumbled. That was exactly the line that cased the error in your > function call. Does the error still occur if you call MEDIPS.createSet in > the same session where get(ls(paste ... worked? > > > Am 20.12.2013 15:53, schrieb Vining, Kelly: > > 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 '$' or '[[' operator to access a given sequence) >> ________________________________________ >> From: bioconductor-bounces@r-project.org [bioconductor-bounces@r- >> project.org] on behalf of Matthias Lienhard [lienhard@molgen.mpg.de] >> Sent: Friday, December 20, 2013 3:32 PM >> To: bioconductor@r-project.org >> Subject: Re: [BioC] separate MEDIPS.createSet required for each >> replicate? RE: using custom BSgenome with MEDIPS >> >> OK, that looks alright. What happens when prompting >> >> BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3" >> library(BSgenome.Ptrichocarpa.Phytozome.v3) >> get(ls(paste("package:",BSgenome, sep=""))) >> >> >> >> >> Am 20.12.2013 15:18, schrieb Vining, Kelly: >> >>> Hi Lukas, >>> Here's the output: >>> >>> BSgenome = "BSgenome.Ptrichocarpa.Phytozome.v3" >>>> ls("package:BSgenome.Ptrichocarpa.Phytozome.v3") >>>> >>> [1] "BSgenome.Ptrichocarpa.Phytozome.v3" "Ptrichocarpa" >>> >>>> get(ls("package:BSgenome.Ptrichocarpa.Phytozome.v3")) >>>> >>> Black cottonwood genome >>> | >>> | organism: Populus trichocarpa (Black cottonwood) >>> | provider: Phytozome (JGI) >>> | provider version: 3.0 >>> | release date: January 2010 >>> | release name: Populus trichocarpa v3.0 >>> | >>> | single sequences (see '?seqnames'): >>> | Chr01 Chr02 Chr03 Chr04 Chr05 Chr06 Chr07 Chr08 Chr09 Chr10 >>> Chr11 >>> | Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 >>> | >>> | multiple sequences (see '?mseqnames'): >>> | scaf >>> | >>> | (use the '$' or '[[' operator to access a given sequence) >>> >>> ________________________________ >>> From: Lukas Chavez [lukas.chavez.mailings@googlemail.com] >>> Sent: Friday, December 20, 2013 2:11 PM >>> To: Vining, Kelly >>> Cc: Lukas Chavez; bioconductor@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@oregonstate.edu<mailto:kelly.vining@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@googlemail.com<mailto:lukas.>>> chavez@googlemail.com>] >>> Sent: Friday, December 20, 2013 1:42 PM >>> To: Vining, Kelly >>> Cc: Lukas Chavez; bioconductor@r-project.org<mailto:>>> bioconductor@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@oregonstate.edu<mailto:kelly.vining@oregonstate.edu>>> ><mailto:kelly.vining@oregonstate.edu<mailto:>>> Kelly.Vining@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@r-project.org<mailto:bioconducto>>> r-bounces@r-project.org><mailto:bioconductor-bounces@r-project.org>>> <mailto:bioconductor-bounces@r-project.org>> [bioconductor- bounces@r- >>> project.org<mailto:bioconductor-bounces@r-project.org><mailto:>>> bioconductor-bounces@r-project.org<mailto:bioconducto>>> r-bounces@r-project.org>>] on behalf of Vining, Kelly [ >>> Kelly.Vining@oregonstate.edu<mailto:kelly.vining@oregonstate.edu>>> ><mailto:kelly.vining@oregonstate.edu<mailto:>>> Kelly.Vining@oregonstate.edu>>] >>> Sent: Friday, December 20, 2013 12:34 PM >>> To: 'Lukas Chavez' >>> Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org>>> ><mailto:bioconductor@r-project.org<mailto:bioconductor@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@googlemail.com<mailto:>>> lukas.chavez.mailings@googlemail.com><mailto:lukas.chavez.>>> mailings@googlemail.com<mailto:lukas.chavez.mailings@googlemail.com>>] >>> Sent: Wednesday, December 18, 2013 12:42 PM >>> To: Vining, Kelly >>> Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org>>> ><mailto:bioconductor@r-project.org<mailto: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<mailto:kelly.vining@oregonstate.edu>>> ><mailto:kelly.vining@oregonstate.edu<mailto:>>> Kelly.Vining@oregonstate.edu>><mailto:kelly.vining@oregonstate.edu>>> <mailto:kelly.vining@oregonstate.edu><mailto:kelly.vining@>>> oregonstate.edu<mailto:kelly.vining@oregonstate.edu>>>> wrote: >>> >>> ________________________________ >>> From: Vining, Kelly >>> Sent: Tuesday, December 17, 2013 10:58 AM >>> To: 'Lukas Chavez' >>> Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org>>> ><mailto:bioconductor@r-project.org<mailto:bioconductor@r-project.org>>> >><mailto:bioconductor@r-project.org<mailto:bioconductor@r-project .org="">< >>> mailto:bioconductor@r-project.org<mailto: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. >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto:>>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org>><mailto:>>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto:>>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org>>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto:>>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org<mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >> >> [[alternative HTML version deleted]] >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]