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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&q...

...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 last is added. Here it the working example for more clarity: ``` library(e1071) library(lattice) library(latticeExtra) make.grid <- function(x, n = 1000) { grange = apply(x, 2, range) x1 = seq(from = grange[1,1], to = grange[2,1], length = n) x2 = seq(from = grange[1,2], to = grange[2,2], length = n) expand.grid(X1 = x1, X2 = x2) } plot_list <- list() for (i in 1:10) { x1 = rnorm(100, mean = 0.2, sd = 0.15) y1 = rnorm(100, mean = 0.7, sd = 0.1...

...9;t manually add them one by one to the plot, so I tried to > loop into them, but only the last is added. > Here it the working example for more clarity: > > ``` > library(e1071) > library(lattice) > library(latticeExtra) > > make.grid <- function(x, n = 1000) { > grange = apply(x, 2, range) > x1 = seq(from = grange[1,1], to = grange[2,1], length = n) > x2 = seq(from = grange[1,2], to = grange[2,2], length = n) > expand.grid(X1 = x1, X2 = x2) > } > > plot_list <- list() > for (i in 1:10) { > x1 = rnorm(100, mean = 0.2, sd = 0.15)...

...#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...

...#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...

...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...

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-pack...

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/Machine...

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 behavior will change due to this...

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]]

...ang :: Rewriter/objc-modern-metadata-visibility.mm Clang :: SemaCXX/warn-loop-analysis.cpp LLVM :: Transforms/SimplifyCFG/bug-25299.ll Next Steps: I plan to extend this behavior to the iteration of other unordered containers (like DenseMap, etc). Thanks, Mandeep On 11/15/2016 3:06 PM, Grang, Mandeep Singh wrote: > 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...

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{en...

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(GenomicRang...

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.

...eration to another container population, and to the final program > output... > > 2) Maybe - but I would think that'd still end up using heuristics to > guess at whether one iteration order impacts the order of another > container, etc. > > On Wed, Aug 8, 2018 at 7:43 PM Grang, Mandeep Singh via llvm-dev > <llvm-dev at lists.llvm.org <mailto:llvm-dev at lists.llvm.org>> wrote: > > In the past, I had added the ability in LLVM to uncover 2 types of > non-deterministic behaviors: iteration of unordered containers with > pointer-like k...

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: