search for: granges

I have a confusing error from R CMD check that I don't get when running the example manually by hand. In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are require(GenomicRanges) annoDF <- as.data.frame(anno) # anno is the GRanges object. and that second line gives: Error in as.data.frame.default(anno) : cannot coerce class 'structure("GRanges&quo...

Hello, I am using e1071 to run support vector machine. I would like to plot the data with lattice and specifically show the hyperplanes created by the system. I can store the hyperplane as a contour in an object, and I can plot one object at a time. Since there will be thousands of elements to plot, I can't manually add them one by one to the plot, so I tried to loop into them, but only the

On Tue, Oct 27, 2020 at 6:04 PM Luigi Marongiu <marongiu.luigi at gmail.com> wrote: > > Hello, > I am using e1071 to run support vector machine. I would like to plot > the data with lattice and specifically show the hyperplanes created by > the system. > I can store the hyperplane as a contour in an object, and I can plot > one object at a time. Since there will be

...#39;enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE) <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL) Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See the chapter 'Writing R documentation files' in manual 'Writing R Ex...

...#39;enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE) <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL) Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See the chapter 'Writing R documentation files' in manual 'Writing R Ex...

...PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 6637 darstr 20 0 30.0g 29g 4712 S 0 63.2 10:34.43 R and what objects I have loaded in memory : > lsos() Type Size PrettySize Rows Columns A list 552387720 526.8 Mb 2 NA B GRangesList 552376408 526.8 Mb 4 NA C SimpleRleList 353421896 337 Mb 24 NA D GRanges 236410608 225.5 Mb 15272853 NA E data.frame 6981952 6.7 Mb 24966 14 F data.frame 6782136 6.5 Mb 24966 13 G list 4393704 4.2 Mb 2...

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

...em with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: > peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100, > downstream = 100, genome = Hsapiens) Error in validObject(.Object) : invalid class "GRanges" object: superclass "Sequence" not defined in the environment of the object's class Is the error coming from my configuration or from the code? I do not know many things about OOP in R. Thanks. -- View this message in context: http://r.789695.n4.nabble.com/chippeakanno-packag...

Ping From: Mandeep Singh Grang [mailto:mgrang at codeaurora.org] Sent: Tuesday, February 03, 2015 4:34 PM To: 'llvmdev at cs.uiuc.edu' Cc: 'ghoflehner at apple.com'; 'apazos at codeaurora.org'; mgrang at codeaurora.org Subject: Question on Machine Combiner Pass Hi, In the file lib/CodeGen/MachineCombiner.cpp I see that in the function

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190 GNN 2 100

On Tue, Dec 13, 2016 at 6:39 PM, Hans Wennborg <hans at chromium.org> wrote: > On Tue, Dec 13, 2016 at 4:57 PM, Grang, Mandeep Singh via llvm-dev > <llvm-dev at lists.llvm.org> wrote: >> Everyone, >> >> The following patch to reverse iterate SmallPtrSet's has now been merged: >> https://reviews.llvm.org/D26718 >> >> This is how LLVM

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]

Everyone, The following patch to reverse iterate SmallPtrSet's has now been merged: https://reviews.llvm.org/D26718 This is how LLVM behavior will change due to this patch: - In LLVM builds with *assertions enabled*, SmallPtrSet's would always be reverse iterated by default. This default behavior can be overridden via the flag "-mllvm -reverse-iterate=<true/false>".

I see that the following test fails if reverse iteration of SmallPtrSet is enabled: /clang/test/SemaCXX/warn-loop-analysis.cpp/ This is because in SemaStmt.cpp we iterate SmallPtrSet and output warnings about the variables not used in the loop. Expected output: /warning: variables 'i', 'j', and 'k' used in loop condition not modified/ Output with reverse iteration:

...anism, seqLen, ...) { ... ... ... }) setMethod("enrichmentCalc", c("GenomeData", "BSgenome"), function(rs, organism, seqLen=NULL, do.warn=FALSE) { ... ... ... }) setMethod("enrichmentCalc", c("GRanges", "BSgenome"), function(rs, organism, seqLen=NULL) { ... ... ... } and a part of my Rd file is : \name{enrichmentCalc} \docType{methods} \alias{enrichmentCalc,GenomeDataList,BSgenome-method} \alias{enrichmentCalc,GenomeData,BSgenome-method} \alias{enri...

Hello, I have start and end coordinates from different experiments (DNase hypersensitivity data) and now I would like to combine overlapping intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101 are combined to 30-101. But 49-101 and 70-103 would not be combined because they are on different chromosomes (chr a and chr b). Does anybody have an idea? Thanks Hermann > df

...chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5 chr1 30 40 11 + I just wondering is there an efficient way to find overlapped, upstream and downstream genes for each gene in the granges For example, assuming all_genes_gr is a ~50000 genes genomic range, the result I want like belows: gene_nameupstream_genedownstream_geneoverlapped_gene gene1NAgene2NA gene2gene1gene4gene3 gene3gene1gene4gene2 gene4gene3gene5NA Currently , the strategy I use is like that, library(GenomicRanges...

Everyone, There is non-determinism in LLVM codegen in the following scenarios: 1. Between back-to-back runs of the same LLVM toolchain 2. Between Release vs Release+Asserts toolchains 3. Between Linux vs Windows toolchains The main reasons for the non-determinism in codegen are: 1. Iteration of unordered containers (like SmallPtrSet, DenseMap, etc) where the iteration order is undefined 2.

Thanks for your response David. 1) I'm not sure it's do-able. I don't know of any nice way to track whether an ordered walk of an unordered container leaks out into the final output of the program. Only iterating over an unordered container is probably not a sufficient hint (it'd have a high false positive rate to warn on every instance of that) - and I don't have any

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow: