similar to: finding overlapping regions

Hi: I have a two large files (over 300K lines). file 1: Name X UK 199 UK 230 UK 139 ...... UAE 194 UAE 94 File 2: Name X Y UK 140 180 UK 195 240 UK 304 340 .... I want to select X of File 1 and search if it falls in range of X and Y of File 2 and Print only those lines of File 1 that are in range of File 2 X and Y How can it be done it

Hi, Is there a mean to automatically choose one version of the 'rbind' function ? By default, R chose the 'rbind' from {base}, i would lke to use the one from {IRanges}... Is it possible to set that using 'par' ? > ?rbind Help on topic 'rbind' was found in the following packages: Package Library IRanges

Hi, when running the following on a fresh R, library("IRanges") annotation showMethods("annotation") Biobase:::annotation showMethods("annotation") I get (see the "^^^^^" marked output at the bottom): > library("IRanges") Carico il pacchetto richiesto: 'IRanges' The following object(s) are masked from package:base :

Dear baseRs, I recently made a mistake when renaming data frame columns, accidentally creating an NA column. I found the following strange behavior when negative indexes are used. Can anyone explain what happens here. No "workarounds" required, just curious. Dieter Version: Windows, R version 2.6.1 (2007-11-26) #----------------------------- df = data.frame(a=0:10,b=10:20) df[,-2]

Dear expeRts, What is the best approach to create a third data frame from two given ones, when the new/third data frame has last column computed from the last columns of the two given data frames? ## Okay, sounds complicated, so here is an example. Assume we have the two data frames: df1 <- data.frame(Year=rep(2001:2010, each=2), Group=c("Group 1","Group 2"), Value=1:20)

Hi there, I have a list of dataframes (generated by reading multiple files) and all dataframes are comparable in dimension and column names. They also have a common column, which, I'd like to use for merging. To give a simple example of what I have: df1 <- data.frame(c(LETTERS[1:5]), c(2,6,3,1,9)) names(df1) <- c("pos", "data") df3 <- df2 <- df1 df2$data

Hi, i'm very new to R, so sorry for what i'm sure is a very basic question. I'm producing a boxplot with the data below: df3<-data.frame( x=c(10,11,115,12,13,14,16,17,18,21,22,23,24,26,27,28,29,3,30,32,33,34,35,4,4 1,45,5,50,52,56,58,6,67,6738,68,7,8,9), fq=c(8,11,1,2,4,4,2,2,6,3,4,2,2,1,1,1,4,51,3,1,1,1,1,35,1,1,19,2,1,1,1,14,1, 1,1,10,13,5),

Hey Folks, Could somebody show me how to loop through a list of dataframes? I want to be able to generically access their elements and do something with them. For instance, instead of this: df1<- data.frame(x=(1:5),y=(1:5)); df2<- data.frame(x=(1:5),y=(1:5)); df3<- data.frame(x=(1:5),y=(1:5)); plot(df1$x,df1$y); plot(df2$x,df2$y); plot(df3$x,df3$y); I would like to do something like:

Hallo Everyone I have the kind of problem that one should never have because one must always plan well and communicate with your team. But now I haven't so here is my problem. I have data coming in on a daily basis from surveys in 10 towns. The questionnaire has 62 variables but some of the regions have used older versions of the questionnaire that have a few variables less. I want to combine

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: ------------------ 1>

Simple illustration, > df3 <- data.frame(id=c(3,2,1,4), age=c(40,50,60,50), dose1=c(1,2,1,2), dose2=c(2,1,2,1), dose4=c(3,3,3,3))> df3 id age dose1 dose2 dose41 3 40 1 2 32 2 50 2 1 33 1 60 1 2 34 4 50 2 1 3> melt.data.frame(df3, id.var=1:2, na.rm=T) id age variable value1 3 40 dose1 12 2 50 dose1 23 1

Hi I'm missing something here but I cannot figure out what. What I can see is that the same code works when I load it via source(...) yet fails when I execute it after loading the package I have built (which includes the code. Below is a transcript of my R session. First I load the code from a file, using source(). Then I execute it fine. Then I remove the function object, I load the

Thank you Michael Dewey. Can you please send me the email id for Bioconductor. regards Pijush On Fri, Dec 29, 2017 at 5:20 PM, Michael Dewey <lists at dewey.myzen.co.uk> wrote: > Dear Pijush > > You might do better to ask on the Bioconductor list as IRanges does not > seem to be on CRAN so I deduce it is a Bioconductor package too. > > Michael > > > On

Dear all, I have some very big data files that look something like this: id chr pos ihh1 ihh2 xpehh rs5748748 22 15795572 0.0230222 0.0268394 -0.153413 rs5748755 22 15806401 0.0186084 0.0268672 -0.367296 rs2385785 22 15807037 0.0198204 0.0186616 0.0602451 rs1981707 22 15809384 0.0299685 0.0176768 0.527892 rs1981708 22 15809434 0.0305465 0.0187227 0.489512 rs11914222 22 15810040 0.0307183

Dear Sir, I have been using R for a long time. But recently I have faced a problem when installing the Bioconductor package named "methyAnalysis". Firstly it was require to update my older R (R version 3.4.3 (2017-11-30)) in to newer version. That time I have also updated the RStudio software. After that when I have tried to install the package named "methyAnalysis". It

Dear Pijush You might do better to ask on the Bioconductor list as IRanges does not seem to be on CRAN so I deduce it is a Bioconductor package too. Michael On 29/12/2017 07:29, Pijush Das wrote: > Dear Sir, > > > > > I have been using R for a long time. But recently I have faced a problem > when installing the Bioconductor package named "methyAnalysis".

Dear group, Here is my df : df3 <- structure(list(DESCRIPTION = c("COPPER May/10", "COTTON NO.2 Jul/10", "CRUDE OIL miNY May/10", "GOLD Jun/10", "ROBUSTA COFFEE (10) Jul/10", "SOYBEANS Jul/10", "SUGAR NO.11 Jul/10", "SUGAR NO.11 May/10", "WHEAT Jul/10", "SPCL HIGH GRADE ZINC USD",

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR

Hello R user, I have several data frames with >100 columns and I did a linear regression over time of each column df1.lm <- lapply(df1, function(x) lm(x~year)$coeff[2]) that worked fine and I get slope of each column oder time - until I divided df1 by df2 df3 <- df1/df2 > df3.lm <- lapply(df3, function(x) lm(x~year)$coeff[2]) Error in lm.fit(x, y, offset = offset, ...) :

I have the following data: prefix <- c("cheap", "budget") roots <- c("car insurance", "auto insurance") suffix <- c("quote", "quotes") prefix2 <- c("cheap", "budget") roots2 <- c("car insurance", "auto insurance") roots3 <- c("car insurance", "auto