User: Tom Oates

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Tom Oates60
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Posts by Tom Oates

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Problem Subsetting ExpressionSet
... I am having trouble subsetting an ExpressionSet via an integer vector as follows: I download an ExpressionSet from GEO to be object a1 pa1<-pData(a1) And then grep the title column of pa1 to retain only a filtered part of the dataset   title geo_accession GSM47561 ...
biobase bioconductor expressionset written 6 months ago by Tom Oates60 • updated 6 months ago by James W. MacDonald45k
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Using Precede in GenomicRanges
... Dear All I have GRanges objects of transcript information (subject) & for regions of interest (query). Top lines of (subject): seqnames ranges strand | tx_id tx_name | [1] 1 [5473, 16844] + | 1 ENSR ...
written 4.6 years ago by Tom Oates60 • updated 4.6 years ago by Valerie Obenchain ♦♦ 6.4k
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ties & strandedness in distanceToNearest GRanges
... Hi I am using distanceToNearest on a datset of CpG dinucleotides and the rat transcripts from the latest ensembl build. Datasets as below: CpGs GRanges with 6 ranges and 4 metadata columns: seqnames ranges strand | | [1] 10 [ 96723746, 967237 ...
go written 4.7 years ago by Tom Oates60 • updated 4.7 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: distanceToNearest in GenomicRanges
... Thanks This works a treat & Is exactly what I was looking for Tom On Mon, Feb 11, 2013 at 6:08 PM, James W. MacDonald wrote: > Hi Tom, > > > On 2/11/2013 11:35 AM, Tom Oates wrote: > >> Hi >> I am very much a learner in R in general& GenomicRanges in general & ...
written 4.8 years ago by Tom Oates60
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distanceToNearest in GenomicRanges
... Hi I am very much a learner in R in general & GenomicRanges in general I am struggling to find documentation to help me get my head around distanceToNearest in GenomicRanges If I have a GRanges object: GRanges with 6 ranges and 4 metadata columns: seqnames ranges strand | ...
genomicranges written 4.8 years ago by Tom Oates60 • updated 4.8 years ago by James W. MacDonald45k
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Comment: C: Using GenomicRanges with table data
... Sorry for not being clear That is indeed what I mean by "levels not matching" So is it true that the chr1..chr2 etc as it appears in Levels will have no effect on further analysis? even though Values & Levels for seqnames do not match? On Fri, Jan 11, 2013 at 1:54 PM, Steve Lianoglou wrote: &g ...
written 4.9 years ago by Tom Oates60
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Using GenomicRanges with table data
... Hi I am trying to use GenomicRanges as part of an anlalysis of sequencing data. I have a number of files which I wish to use to make GRanges objects. For example: chr1 579578 579804 CpG_12 chr1 630418 630623 CpG_11 chr1 804552 804763 CpG_9 chr1 1307051 1307362 Cp ...
iranges genomicranges written 4.9 years ago by Tom Oates60 • updated 4.9 years ago by Steve Lianoglou12k

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