R: when to use setGeneric or export a s4 method in the namespace
In an R session with only the base packages and methods loaded you can see that the generic for "[" is defined, and the generic for "as.list" is not > getGeneric("[") standardGeneric for "[" defined from package "base" function (x, i, j, ..., drop = TRUE) standardGeneric("[", .Primitive("[")) <bytecode: 0x28f7990>...
How to create GRange object for a large dataset
Use makeGRangesFromDataFrame() with keep.extra.columns=TRUE. Alternatively create the GRanges as above, then add mcols() dropping uninteresting columns. mcols(gr) = reference[,-(1:3)] Feel free to ask questions about Bioconductor packages on the Bioconductor support forum....
p.adjust with n < than number of tests
The code: p.adjust # typed at command line prints out the code # copy the body of the function ... is really very simple and all R. Just redefine a function that comments out that stopifnot() line: my.p.adj <- function (p, method = p.adjust.methods, n = length(p)) # paste the...
Understanding an RLE coverage value
Probably it's better to ask about Bioconductor packages on the Bioconductor support site. The interpretation is that there is a run of 25 nucleotides with 0 coverage, then a run of 24 nucleotides with 1 coverage (i.e., a single read) then another run of 249 nucleotides with no coverage, then...
Concatenating positions into genomic segments
r,concatenation,bioinformatics,bioconductor,genome
I couldn't think of any pretty solution using basic dataframe manipulation, so here's a bad-looking one that works: First, add stringsAsFactors to df creation: df <- read.table(text=df, header=T, stringsAsFactors = FALSE) start <- df$Position[1] end <- integer() output <- NULL count <- 1 for (i in 1:(nrow(df)-1)) { if(df$Bel[i] <...
Creating a loop to use read.eset in bioconductor
Ah - just spotted the error - you must remove quotes from around the "ffdat" on the final line, and same for the "expr"
R, biocLite, error installing DESeq2
From the log, it seems that the problem originated from XML package. XML package fails to compile if libxml2 library is not available. To install it on Linux: sudo apt-get install libxml2 sudo apt-get install libxml2-dev Then rerun the installation....
makeContrast between two different sets of data
as you have a problem of class comparison between two classes I suggest you to read the user guide of the limma package of Bioconductor, which is a popular package for identification of differentially expressed genes (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf). You can focus on section 9.2 if you are working with one-color microarrays....
How can I convert Ensembl ID to gene symbol in R?
r,data.frame,bioinformatics,bioconductor
This is because the values you have in your gene column are not gene ids, they are peptide id (they start with ENSP). To get the info you need, try replacing ensembl_gene_id by ensembl_peptide_id: G_list <- getBM(filters= "ensembl_peptide_id", attributes= c("ensembl_peptide_id", "entrezgene", "description"),values=genes,mart= mart) Also, what you are really looking for...
How to exclude packages for updating in R?
You can prepare an "updatable" list of packages, then call biocLite blacklist <- c("pkga", "pkgb") installed <- rownames(installed.packages()) updatable <- installed[!installed %in% blacklist] biocLite(updatable) ...
RGraphiz installation keeps on failing ubuntu 12.04
After correspondence with the package maintainer, I found out that the most recent commit was not pushed to github yet. This issue is now resolved and installing from github works flawlessly: install_github("kasperdanielhansen/Rgraphviz") The problem was caused by some agressive compiler settings used on Ubuntu 12.04. It was solved in commit...
Is it insecure to execute code via an HTTP URL?
r,security,bioinformatics,bioconductor,man-in-the-middle
Yes, you are correct. Loading executable code over a cleartext connection is vulnerable to a MITM. Unless loaded over HTTPS where SSL/TLS can be used to encrypt and authenticate the connection, or unless the code has been signed and verified at the client then a MITM attacker could alter the...
Subset SAM/BAM file in R
r,subset,bioinformatics,bioconductor
It's probably more convenient to input the data with GenomicAlignments::readGAlignments, including the qname by specifying param=ScanBamParam(what="qname") as an argument. You could then subset with %in%. Here's a more complete example, using one of the ExperimentData packages library(GenomicAlignments) library(RNAseqData.HNRNPC.bam.chr14) fname <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1] want <- c("ERR127306.11930623", "ERR127306.24720935", "ERR127306.23706011", "ERR127306.22418829", "ERR127306.13372247", "ERR127306.20686334",...
write a function that check whether a package has been install in R system
Use tryCatch. Here is an example: # purpose: write a function to: # - attempt package load # - if not then attempt package install & load checkInstallPackage = function(packName) { tryCatch(library(packName), error = function(errCondOuter) { message(paste0("No such package: ", packName, "\n Attempting to install.")) tryCatch({ install.packages(packName) library(packName, character.only =...
Not able to executing all text files from one folder by a Rscript
Give the full path of the folder under path as below: scanFiles<-dir(path='/path/to/folder/',pattern = ".*.txt$") ...
R CMD check warning with CUDA *.cu files
While the default behaviour of nvcc is to automatically deduce language from filename extension (so that CUDA code is expected to be contained in a .cu extension file), this is not a fixed requirement. nvcc supports the -x flag to manually set language for a given compilation unit, so you...
LiftOver in R (error)
r,apply,data-conversion,bioconductor,genome
This is just a warning, not an error. A simple web search found: https://www.biostars.org/p/122005/...
merge two data.frame with condition in R
May be this helps library(data.table) setkey(setDT(df1),chr, Start, End) setkey(setDT(df2), chr, Start, End) res <- foverlaps(df1, df2, type='any')[ ( Start > i.Start| End> i.End)|is.na(Start)][, c('Start', 'End') := list(i.Start, i.End)][,7:8 := NULL] dcast(res, ...~ID, value.var='Xp', fill=0)[, -7, with=FALSE] # chr Start End Gene S8411 S8413 #1: 4 1000 1105 Gm12724 0.312 0.000...