IRanges

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Convert IRangesOverview.Rnw to IRangesOverview.Rmd

2

@jwokaty please review this PR I have reviewed it once using the checklist and make sure that `R CMD build` contains html. After your review we will ask @hpages for...

sonali8434

It would do `compress=TRUE` if the input is not too big, otherwise it would fallback to `compress=FALSE`. For example: ``` RleList(Rle(8, 2e9), Rle(5, 200), compress=NA) ``` would do `RleList(Rle(8, 2e9),...

hpages

Hi Herve, Here is the pull request for fixing ALTREP problem in IRange constructor. The main changes are: 1. Use GET/SET function to access data from a vector 2. Remove...

Jiefei-Wang

Large numbers are often divided into groups using a delimeter to ease of reading. English often uses comma to create groups of three for thousands, millions etc. IUPAC and International...

balwierz

See the Biostars thread at: https://support.bioconductor.org/p/9140415 I have checked the fix proposed by story.benjamin and this fixes the behaviour of the function and would propose a fix Correct function below:...

AxelRosendahlHuber

Subsetting a SimpleRleList object by a GRanges object 'x' should work, even when 'sum(width(x))' >= 2^31

1

This is a spin-off from issue #43: ``` library(BSgenome.Hsapiens.UCSC.hg38) genome

hpages

Add rescale() for IRanges objects

2

``` library(IRanges) .zoom0 length(x) && length(z) != 1L) stop("'z' is longer than 'x'") if (anyNA(z) || min(z)

hpages

``` library(IRanges) x1

hpages

Make the IRanges() constructor compatible with ALTREP

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(Moving this from the devteam-bioc Slack to GitHub) Jiefei wrote on Slack: > Hi Herve, I would like to make some changes to the IRanges package but I might miss...

hpages

propagate mcols() through setOps where possible

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Just an idea -- where possible, propagate mcols(). For example, `mcols(c(a,b)) = rbind(mcols(a), mcols(b))` (IRanges already does this) `mcols(intersect(a,b))[i, ] = cbind(mcols(a)[j, ], mcols(b)[k, ])` where j is the row...

rcorty