## User: balwierz

balwierz40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
1 year, 6 months ago
Joined:
3 years, 8 months ago
Email:
b*******@gmail.com

#### Posts by balwierz

<prev • 11 results • page 1 of 2 • next >
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... I will describe the problem using GRanges, but it is solely within IRanges. Ranges of width are apparently allowed. You can obtain them for instance calling promoters(TxDb, upstream=0, downstream=0)     Specifically, these ranges cannot be found by distanceToNearest _if_ they are within the su ...
written 20 months ago by balwierz40 • updated 19 months ago by Hervé Pagès ♦♦ 13k
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... Merci                   ...
written 20 months ago by balwierz40
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... After 2 years it is still broken. This time IRanges introduce faulty code. a <- "foo" ifelse(is.numeric(a), yes=a+5, no=a) [1] "foo" library(IRanges) ifelse(is.numeric(a), yes=a+5, no=a) Error in a + 5 : non-numeric argument to binary operator   ...
written 22 months ago by balwierz40
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... Hello Herve, I just bumped into this thread after an hour of debugging my code, which wasn't broken. ifelse is broken. Not any more in S4vectors, but the code turning base function ifelse to a S4 function dispatched by all 3 arguments still exists in IRanges. Moreover, when I load IRanges there is ...
written 22 months ago by balwierz40
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...   class(inputR) [1] "GRanges" attr(,"package") [1] "GenomicRanges" class(chipR) [1] "GRanges" attr(,"package") [1] "GenomicRanges" raw.output = bayespeak(as(chipR, "RangedData") , as(inputR, "RangedData")) Error in as.vector(x, mode) : invalid 'mode' argument Enter a frame number, or 0 to exit ...
written 2.7 years ago by balwierz40
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... ?som includes a description of class 'som'. component code a metrix with nrow = xdim*ydim, each row corresponding to a code vector of a cell in the map. The mapping from cell coordinate (x, y) to the row index in the code matrix is: rownumber = x + y * xdim should say rownumber = x + y * xdi ...
written 3.1 years ago by balwierz40
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... It would be useful to have more flexibility in selecting the TSS region. It is currently hardcoded in getGenomicAnnotation that the region is subdivided into 1000 bp regions. For some marks and compact genomes it is too large. I would like to have a way to specify bins myself, e.g. by specifying a ...
written 3.2 years ago by balwierz40 • updated 3.2 years ago by Guangchuang Yu1.1k
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... Length of a region is calculated as end - start, instead of end - start + 1. This causes problems when length of a region equals no_windows. I also suggest either checking this condition before CPU intensive operations on a bam file, using warnings instead of stop, or solving the problem properly ...
written 3.2 years ago by balwierz40
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... Steps to reproduce: "log in" -> "with StackExchange ID" -> (log in to your account) -> (approve permission) After that there is an error message giving no details of the problem.   With google ID works without problems ...
written 3.2 years ago by balwierz40
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... Well, I know THAT. The point is import function calls parseURI on strings which are likely not to be URIs. ...
written 3.7 years ago by balwierz40

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