genomation
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BIMSBbioinfo
R package for genomic feature analysis and visualization
Hi, I have been exploring your package for annotation, and have a question: When we use `annotateWithGeneParts`, it outpus a `AnnotationByGeneParts` object which primarily contains promoter/exon/intron/intergenic percentages. However, is there...
I have been using the readBed feature of genomation to read Bed files into R for use in Enriched Heatmaps. Recently I have been getting a parsing failures error, ie.:...
I am analysing some low resolution data and need 1000 bins of 1kb each (covering 1MB in total). My estimation for size of such an object would be roughly `1000...
The hack introduced in https://github.com/BIMSBbioinfo/genomation/issues/141 breaks the possibility of subsetting elements of ScoreMatrixList by names. ```r > foo = ScoreMatrixList(list(first=as(matrix(1), "ScoreMatrix"), second=as(matrix(2,nrow=2,ncol=2), "ScoreMatrix"))) > foo["second"] Error in ScoreMatrixList(tmp) : windows...
The bed file is downloaded from UCSC. A previous version of the package (1.12) has no issues with reading it but 1.14 fails with the "error in rownames ... invalid...
On the Bioc Meeting 2018 people advertised SummarizedExperiment R package for working on matrix-like objects. I got suggestions to check out Delayedarrayes and to think about integrating it to genomation....
Not sure if this is a problem with genomation or some R "feature": If I have a list of score matrices the printout of the list (when typed the name...
heatMeta invisibly returns a meta profile of a score matrix. If that is the only reason a user runs heatMeta, then the graphics produced is just a nuisance and takes...
findFeatureComb with one input element produces error when use.names=TRUE library(GenomicRanges) library(genomation) tab.test = system.file('unitTests/tab.test1', package='genomation') #1. test regular bed input r1 = readGeneric(tab.test) l1 = GRangesList(r1 = r1) comb1 =...
when the target vector is negative (i.e. negative fold changes), is.noCovNA gives wrong results - it converts all < 0 values to NA
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R package for genomic feature analysis and visualization