similar to: DNA sequence Fst

I've installed (maybe not sucessfully) wine 20041201, fst 1.6 and jack_fst-1.2. I'm using jack-0.99 When I try and execute jack_fst such as: #jack_fst Crystal.dll I receive the following error: err:dosmem:setup_dos_mem Cannot use first megabyte for DOS address space, please report can't connect to JACK I assume that the first error message is from wine. Is that true? I

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

I want to create a MDS plot with pairwise Fst values derived from a population genetics project. My Fst values are in a tab-delimited file (lower triangle only) that I view with Excel. When I use the cmdscale command I get the message: Error in cmdscale(x) : Distances must be result of dist or a square matrix In addition: Warning messages: 1: "^" not meaningful for factors in:

Hi, (Sorry for the cross-posting.) After manually installing the 32-bit libjack packages on my 64-bit system, the original problem ("Can't connect to JACK") is gone; now I get a whole new set of errors instead :) When I try to start the Kontakt 5 VST from festige (via fst, via WINE), this is what I get: ============================ ----------------yo... lets see...

Over the last several days, I've been working hard to get all of the Fedora R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and R-rtracklayer, I believe everything is built and updated to the latest versions. And of those packages, they're all ready to go when Fedora infrastructure is working reliably

I am aware of the R Genetics Project that developed the R library and software called Bioconductor (http://www.bioconductor.org/ ) . How do the two relate to each other? What is the one that the other is not and vice versa? Can anybody link me to something that answers the question? -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

I'm trying to put two plots side-by-side in two panels. Since the y-axis of the two plots is the same, I want to leave out the y-axis of the second plot. And the two plots look quite separate from each other. Is there any way to have them stay closer to each other? I've tried to adjust mar option of par but it has a global effect as I see the left margin of the first plot will be

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function

Hello, Everyone, how to use "loop" to make the process automatic and fast? When compute each sample, the script type in R almost the same, just the input and output file's name is changed(chr1 change to chr2, chr3,chr4...). The first sample's script like this: >chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= )

Dear List members I want to do the sliding window analysis of some specific values. Here is my code: require(zoo) dat <- read.table("chr1.txt", header = TRUE, sep="\t") dat2 <- cbind(dat[1,3]) #The first column is also important. It represents the position of the site on the chromosome. TS <- zoo(c(dat2)) a <- rollapply(TS, width=1000000, by=200000, FUN=mean,

Hi, I am currently building an R package and I am facing a peculiar problem where some of the functions does not work within the package. However, if I source the script the function works. For example, in a method for parallelization of analysis on each chromosome simultaneously I am receiving error at the following position of the code: # this profile the information chromosome wise and

Dovecot-2.0.3 reported: Error: Maildir: Found unwanted directory /path/to/mail/user/cur/:2,FST, but rmdir() failed: Directory not empty and sure enough, this directory really does exist and contain a valid message file: # cd /path/to/mail/user/cur/ # ls -lR total 384 drwx------ 8 vmail vmail 272 Sep 24 09:06 . drwx------ 13 vmail vmail 442 Sep 24 09:06 .. -rw------- 5 vmail vmail

Buenas tardes, Tengo un gráfico de dispersión y quiero indicar cada punto a qué individuo corresponde. ¿Cómo añado estas etiquetas de datos? El código es: res<-cmdscale(fst,k=2) plot(res[,1],res[,2],lwd=2,xlab="x",ylab="y") abline(h=0,v=0,col="blue") Muchas gracias, Gemma [[alternative HTML version deleted]]

Hi, My objective is to calculate "Relative (Cumulative) Frequency of Event Occurrence" - something as follows: Sample.Number 1st.Fly 2nd.Fly Did.E.occur? Relative.Cum.Frequency.of.E 1 G B No 0.000 2 B B Yes 0.500 3 B G No 0.333 4 G B No 0.250 5 G G Yes 0.400 6 G B No 0.333 7 B B Yes 0.429 8 G G Yes 0.500 9 G B No 0.444 10 B B Yes 0.500 Please refer to the code below:

Hi, Did you try install.packages('stats'). Let we know about your Sys.info() Karim On Fri, Jan 12, 2018 at 5:37 PM, imane hajar <imane.chafiki.fst at gmail.com> wrote: > hello , > > i am so sorry , i figure it out. > > im sending this msj to the moderator to stop the approval of the mail . > > have a good day. > > > 2018-01-12 15:42 GMT+00:00 imane

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that

Hello, I can't find a package which calculates Kendall's tau-c. There is the package Kendall, but it only calcuates Kendall's tau-b. Here is the example from ttp://www2.chass.ncsu.edu/garson/pa765/assocordinal.htm. cityriots <- data.frame(citysize=c(1,1,2,2,3,3), riotsize=c(1,2,1,2,1,2), weight=c(4,2,2,3,0,4)) cityriots <- data.frame(lapply(cityriots,function(x)

Hi, Found in the man page for update.packages: repos: character vector, the base URL(s) of the repositories to use, i.e., the URL of the CRAN master such as ?"http://cran.r-project.org"? or its Statlib mirror, ?"http://lib.stat.cmu.edu/R/CRAN"?.Can be ?NULL? to install from local files (?.tar.gz? for source packages). - Using