User: Paul Theodor Pyl

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Posts by Paul Theodor Pyl

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[ggbio+GenomicRanges] auto-plotting GRanges in R-devel fails
... Hi all, I observe the following behaviour in my R-devel when I try to autoplot a GRanges with ggbio: > library(ggbio) > library(GenomicRanges) > autoplot( GRanges( Rle("10",1), ranges=IRanges( start = 1000, width=110 ) ) ) Error in start(range(object, ignore.strand = TRUE)) : error ...
written 5.0 years ago by Paul Theodor Pyl80 • updated 5.0 years ago by Tengfei Yin420
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[IRanges] Strange behaviour of global DataFrame with subset in function
... Hi all, I have observed some strange behaviour when I use subset inside a function on a DataFrame that is a global variable, see the example below: > library(IRanges) # [...] > ir_df = DataFrame( x=rnorm(10) ) > old_df = as.data.frame( ir_df ) > a_function = function( cut_off ) sub ...
written 5.0 years ago by Paul Theodor Pyl80 • updated 5.0 years ago by Michael Lawrence9.8k
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Answer: A: ggplot2 and the legend
... Hi Peter, below a small example that I think creates what you want: ggplot( data.frame( value=rnorm(100), rank=1:100, col=rep(c("blue","green"), 50) ) ) + geom_point( aes(y=value, x=rank, colour=col, shape=col) ) + scale_colour_manual( values=c("blue","green") ) The result looks like this for me: ...
written 5.1 years ago by Paul Theodor Pyl80
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[VariantAnnotation] subsetting VCF objects
... Hi all, I am reading in some .vcf files with the readVcf function and realized that I cannot subset the resulting VCF objects if the info field is empty, see example below. Is there a workaround except for loading the info at least partially? Thanks, Paul The Example: > vcf_full = readVcf("t ...
written 5.1 years ago by Paul Theodor Pyl80 • updated 5.1 years ago by Valerie Obenchain ♦♦ 6.4k
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[Gviz] Plot Segmentation
... Hello, I have a question, I used to plot my genomic data with GenomeGraphs where I used trackOverlay to add a Segmentation track to a BaseTrack to create something like this: Can Gviz do something like this also, I did not find any straightforward method in the available documentation, maybe usin ...
gviz written 5.6 years ago by Paul Theodor Pyl80
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VariantAnnotation locateVariants - meaning of precedesID and followsID
... Hi, I have a question concerning the meaning of precedesID and followsID in the result of the locateVariants function from the VariantAnnotation package. The reference manual states: precedesID: The id of the gene the query precedes. Only present for ?intergenic? variants. followsID: The id of th ...
bsgenome transcriptdb genomicfeatures written 5.7 years ago by Paul Theodor Pyl80 • updated 5.7 years ago by Valerie Obenchain ♦♦ 6.4k
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Looks like a bug in GenomicRanges::.breakTie
... Hi, I encountered (during a call to VariantAnnotation::locateVariants) an error that originated from GenomicRanges::.breakTie. From the source code of that function (svn revision 64480) it looks like equivalue can only ever have a length of 1 while equidist can be longer which breaks the call to Da ...
written 5.7 years ago by Paul Theodor Pyl80 • updated 5.7 years ago by Valerie Obenchain ♦♦ 6.4k
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[biomaRt] contradicting gene information
... Hi Guys, I observed the following in a dataset I'm working on: > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > getBM( attributes = c("ensembl_gene_id", "chromosome_name", "strand", "start_position", "end_position"), filters = "ensembl_gene_id", values = c("ENSG00000002586 ...
written 6.0 years ago by Paul Theodor Pyl80 • updated 6.0 years ago by Steve Lianoglou12k

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