exomeCopy tutorial steps

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Brett Spurrier ▴ 10

@brett-spurrier-6334

Last seen 9.6 years ago

Hi there, I am trying to use *exomeCopy* to discover any CNVs in a particular gene (although analyzing the entire exome is idea). I am stepping through the R steps found in: http://bioconductor.org/packages/devel/bioc/vignettes/exomeCopy/inst/d oc/exomeCopy.pdf but I get lost when I reach the line: counts[["GC.sq"]] <- example.counts$GC^2 I have no idea where example comes from? And it's referenced in later steps as well. Can someone help me figure out what or where the example object should come from? Thanks! Brett [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.3 years ago by Vincent J. Carey, Jr. 6.7k • written 10.3 years ago by Brett Spurrier ▴ 10

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Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 5 weeks ago

United States

On Wed, Jan 15, 2014 at 7:41 PM, Brett Spurrier <brett.spurrier@gmail.com>wrote: > Hi there, > > I am trying to use *exomeCopy* to discover any CNVs in a particular gene > (although analyzing the entire exome is idea). > > I am stepping through the R steps found in: > > http://bioconductor.org/packages/devel/bioc/vignettes/exomeCopy/inst /doc/exomeCopy.pdf > > but I get lost when I reach the line: > counts[["GC.sq"]] <- example.counts$GC^2 > > the author should respond, but my guess is that this is just an error in the vignette, as this part comes from an eval=FALSE section. example.counts is undefined at that point in the code chunk; i think "counts" is intended, as counts$GC has just been defined, and this is just a squaring and saving of that quantity. if you look further down in the vignette there are executable lines involving example.counts where this variable seems to be properly defined > I have no idea where example comes from? And it's referenced in later steps > as well. > > Can someone help me figure out what or where the example object should come > from? > > Thanks! > Brett > > [[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]]

ADD COMMENT • link 10.3 years ago Vincent J. Carey, Jr. 6.7k

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Thanks for catching this, I've fixed this now. It should read counts[["GC.sq"]] <- counts$GC^2 and, two lines below counts[["width"]] <- width(counts) âMikeâ On Thu, Jan 16, 2014 at 6:18 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > On Wed, Jan 15, 2014 at 7:41 PM, Brett Spurrier <brett.spurrier@gmail.com> >wrote: > > > Hi there, > > > > I am trying to use *exomeCopy* to discover any CNVs in a particular gene > > (although analyzing the entire exome is idea). > > > > I am stepping through the R steps found in: > > > > > http://bioconductor.org/packages/devel/bioc/vignettes/exomeCopy/inst /doc/exomeCopy.pdf > > > > but I get lost when I reach the line: > > counts[["GC.sq"]] <- example.counts$GC^2 > > > > > the author should respond, but my guess is that this is just an error in > the vignette, as this part comes from an eval=FALSE section. > > example.counts is undefined at that point in the code chunk; i think > "counts" > is intended, as counts$GC has just been defined, and this is just a > squaring and > saving of that quantity. if you look further down in the vignette there > are executable > lines involving example.counts where this variable seems to be properly > defined > > > > > I have no idea where example comes from? And it's referenced in later > steps > > as well. > > > > Can someone help me figure out what or where the example object should > come > > from? > > > > Thanks! > > Brett > > > > [[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]]

ADD REPLY • link 10.3 years ago Michael Love 41k

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