similar to: Failed to locate 'weave' output file / vignette product does not have a known filename extension

Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this:

Thanks to David and Jorge - both of your helpful suggestions got me to the desired endpoint. In case anyone else has this question: I boxplotted my y variable data, but did the "cut" operation on the x variable in order to conserve the order of the y data. I see another suggestion coming in from another user that basically says this. So, my working line of code was: boxplot(count$RPKM

Dear UseRs, I'm making box plots from a data set that looks like this: Chr Start End GeneDensity ReadCount_Explant ReadCount_Callus ReadCount_Regen 1 1 1 10000 107.82 1.243 1.047 1.496 2 1 10001 20000 202.50 0.835 0.869 0.456 3 1 20001 30000 158.80 1.813 1.529 1.131

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

This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search path is excessive and importing selectively is preferable. Let us say my package A either uses a class B (by producing an object that has B embedded as a slot) from another package or provides a

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

Thanks to both Weidong and David for the help! By implementing both of your suggestions I was able to make this work. I did end up putting header=TRUE for both read operations. --Kelly ________________________________________ From: David Winsemius [dwinsemius at comcast.net] Sent: Tuesday, August 30, 2011 1:16 PM To: Vining, Kelly Cc: Weidong Gu; r-help at r-project.org Subject: Re: [R] column

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".

Hi all, I have been struggling with this problem for a few days. I have a data table like this: gene rpkm1 diff1 rpkm2 diff2 gene1 23 50 13 120 gene2 111 220 827 1200 gene3 75 998 71 910 And I want to re-format it so that, for each gene, I have a 2x2 contingency table, such as: gene rpkm diff gene1 23 50 gene1 13 120 gene2 111 220 gene2 827

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

Thanks for your help, Rui! That works and will save me a lot of trouble. --Kelly -----Original Message----- From: Rui Barradas [mailto:ruipbarradas at sapo.pt] Sent: Tuesday, July 10, 2012 2:24 AM To: Vining, Kelly Cc: r-help at r-project.org Subject: Re: [R] boxplot with "cut" Hello, Maybe this iss what you're looking for. GD is your data.frame. multi.boxplot <-

Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very much. Best, Guanfeng Wang [[alternative HTML version

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

Dear Michael, I was looking up the status of the cran2deb effort and notice that you now have a PPA where new packages are landing and being built for Ubuntu. It looks like this is still a work in progress, but is already a fantastic resource for me and I hope it is something that you can continue to operate. I'm now installing many of these packages but some things I need are missing.

Dear list, Inspired by the original Knuth tools, and for paedaogical reasons, I wish to produce a document presenting some source code with interspersed comments in the source (see Knuth's books rendering TeX and metafont sources to see what I mean). I seemed to remember that a code chunk could be defined piecewise, like in Comments... <<Chunk1, eval=FALSE, echo=TRUE>>=

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

Currently Makefiles for vignettes are only supported for .tex files. Could the tools package be modified to allow file extensions to be specified for a vignette engine? Having the pandoc pdf conversion in a Makefile rather than through R would be tidier in some cases. If I specify my vignette engine as ``` tools::vignetteEngine( 'myengine', pattern = '\\.[Rr](md|nw)$',

If I understand correctly, all vignettes in a package are built in the same R process. Global options, loaded packages, etc., in an earlier vignette persist in later vignettes. This can introduce user confusion (e.g., when a later vignette builds successfully because a package is require()'ed in an earlier vignette, but not the current one), difficult-to-identify bugs (e.g., when a setting

Interesting, yesterday I had exactly this problem, but today I solved it (see the R-pkg-devel list) by _installing_ R-devel and > update.packages(checkBuilt = TRUE) I also tried it on Martin's Fedora 26 example below. Worked fine (had to install some packages...) On ubuntu 16.04. G?ran Brostr?m On 2017-12-06 11:29, Martin Maechler wrote: >>>>>> Pearce, Robert