User: RichardJActon

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Posts by RichardJActon

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Comment: C: Using GenomicDataCommons R package to identify cases with both DNA methylation a
... Thanks again. I was hoping that I was missing something and API would support more complex conditional queries as I have some moderately complex requirements for the subset of samples i'm after. ...
written 27 days ago by RichardJActon30
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Comment: C: Using GenomicDataCommons R package to identify cases with both DNA methylation a
... Thanks Sean and Kevin, I was caught out by the 'filter()' behaviour, but picked up on it during a re-read of the vignette. However if I have understood the above correctly This will list all cases with either "Solid Tissue Normal" or "Blood Derived Normal" and either "gene_expression" __or__ "methyl ...
written 27 days ago by RichardJActon30
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Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
... I'm trying to get a list of cases for which there is DNA methylation and gene expression data available for both normal and cancer tissue samples using the GenomicDataCommons R package (which I am using for the first time). qCases <- cases() %>% filter( ~ samples.sample_type == "Solid Ti ...
R rna-seq dna methylation gdc written 28 days ago by RichardJActon30 • updated 28 days ago by Sean Davis21k
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Comment: C: Gviz title panel text offset
... Oh apparently you can paste and image into the question composition field and it does not get put in the question but does use up the character limit by being converted into a base64 string how irksome. ...
written 21 months ago by RichardJActon30
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Gviz title panel text offset
... I am creating a Gviz plot with some particularly long titles in the title panel. I tried setting title.width wider and using rotate.title however it appears that rotate.title rotates about some point in the title. Possibly the midpoint but clearly not the first character of the title, consequently ...
gviz written 21 months ago by RichardJActon30
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Comment: C: Splitting a GRanges object into List of GRange objects by position.
... Thanks Mike, That seems to do exactly what I wanted. I'm not sure I understand how though. looking at the output of `as.factor(gr)` I can see why it works with as.factor but not why it would work without? I had not expected that behaviour from as.factor as applied to a GRanges object, thought th ...
written 21 months ago by RichardJActon30
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Splitting a GRanges object into List of GRange objects by position.
... I have a GRanges object and I would like to get a list of GRange objects which are subsets of the original object, each of the the objects in this list should have the same position (same chr, start and end values).   library(GenomicRanges) # input: gr=GRanges(seqnames=c("chr1","chr1","chr2","chr ...
granges grangeslist R group subsett written 21 months ago by RichardJActon30 • updated 21 months ago by Mike Smith3.1k

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Popular Question 20 months ago, created a question with more than 1,000 views. For Splitting a GRanges object into List of GRange objects by position.

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