htSeqTools - naming RangedData objects?

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Ian Donaldson ▴ 70

@ian-donaldson-4761

Last seen 9.6 years ago

I am trying to get htSeqTools to create a PCA for my ChIP-seq sample reads. However, by default there are no labels associated with the sample points in my PCA plot. METHOD: I created RangedData objects like this, e.g: RR05 <- readAligned(dirPath , "RR_20111013_filtered_RR05_bfast_hg18_a3 _best_unique_sorted_mapped.bam", type='BAM') RR05ranges <- RangedData(ranges=IRanges(position(RR05),position(RR05)+width(RR05)), space=chromosome(RR05), strand=strand(RR05)) I have assigned my RangedData to a list like this: samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges) Can i assign names like this? names(samples) <- c("RR05","RR06","RR2_03", "RR2_04") It works, but my worry is that the order might be different if objects do not have a fixed order..... Or is there a way of assigning a name to each RangedData object before they are added to a list? Thank you! As you can tell i am no expert at using R/Bioconductor! Ian [[alternative HTML version deleted]]

htSeqTools ASSIGN htSeqTools ASSIGN • 1.2k views

ADD COMMENT • link updated 12.3 years ago by Michael Lawrence ★ 11k • written 12.3 years ago by Ian Donaldson ▴ 70

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

On Tue, Jan 17, 2012 at 8:22 AM, Ian Donaldson < Ian.Donaldson@manchester.ac.uk> wrote: > I am trying to get htSeqTools to create a PCA for my ChIP-seq sample > reads. However, by default there are no labels associated with the sample > points in my PCA plot. > > METHOD: > I created RangedData objects like this, e.g: > RR05 <- readAligned(dirPath , > "RR_20111013_filtered_RR05_bfast_hg18_a3_best_unique_sorted_mapped.b am", > type='BAM') > > RR05ranges <- > RangedData(ranges=IRanges(position(RR05),position(RR05)+width(RR05)), > space=chromosome(RR05), strand=strand(RR05)) > > I have assigned my RangedData to a list like this: > samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges) > > Can i assign names like this? > names(samples) <- c("RR05","RR06","RR2_03", "RR2_04") > > Yes. > It works, but my worry is that the order might be different if objects do > not have a fixed order..... > > The objects do have a fixed order, and the names will be kept in sync. > Or is there a way of assigning a name to each RangedData object before > they are added to a list? > > You can always name the arguments to the RangedDataList function, like RangedDataList(A = rd_a, B = rd_b). > Thank you! As you can tell i am no expert at using R/Bioconductor! > > I might also point you towards the use of readGappedAlignments in GenomicRanges. A GappedAlignments can be coerced to a GRanges with grlist() and then on to RangedData via as(). You could put the GRanges in a GenomicRangesList in the same way as RangedDataList; however, htSeqTools might not work with that. Ian > > > [[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 12.3 years ago Michael Lawrence ★ 11k

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A brief note, htSeqTools does provide methods for GRanges objects. Best, David -----Original Message----- From: Michael Lawrence <lawrence.michael@gene.com> Date: Tue, 17 Jan 2012 09:44:45 To: Ian Donaldson<ian.donaldson@manchester.ac.uk> Cc: bioconductor@r-project.org<bioconductor@r-project.org>; David Rossell<david.rossell@irbbarcelona.org> Subject: Re: [BioC] htSeqTools - naming RangedData objects? On Tue, Jan 17, 2012 at 8:22 AM, Ian Donaldson < Ian.Donaldson@manchester.ac.uk> wrote: > I am trying to get htSeqTools to create a PCA for my ChIP-seq sample > reads. However, by default there are no labels associated with the sample > points in my PCA plot. > > METHOD: > I created RangedData objects like this, e.g: > RR05 <- readAligned(dirPath , > "RR_20111013_filtered_RR05_bfast_hg18_a3_best_unique_sorted_mapped.b am", > type='BAM') > > RR05ranges <- > RangedData(ranges=IRanges(position(RR05),position(RR05)+width(RR05)), > space=chromosome(RR05), strand=strand(RR05)) > > I have assigned my RangedData to a list like this: > samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges) > > Can i assign names like this? > names(samples) <- c("RR05","RR06","RR2_03", "RR2_04") > > Yes. > It works, but my worry is that the order might be different if objects do > not have a fixed order..... > > The objects do have a fixed order, and the names will be kept in sync. > Or is there a way of assigning a name to each RangedData object before > they are added to a list? > > You can always name the arguments to the RangedDataList function, like RangedDataList(A = rd_a, B = rd_b). > Thank you! As you can tell i am no expert at using R/Bioconductor! > > I might also point you towards the use of readGappedAlignments in GenomicRanges. A GappedAlignments can be coerced to a GRanges with grlist() and then on to RangedData via as(). You could put the GRanges in a GenomicRangesList in the same way as RangedDataList; however, htSeqTools might not work with that. Ian > > > [[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 12.3 years ago David Rossell ▴ 100

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