search for: loci

...put in the results in a matrix that is 5 columns wide and 8 rows long (called "result"). # I can get the operation to run but it gives me the results for the last pair of columns and overwrites # the results into every column of my result matrix. I am puzzled as to why this is occurring. Loci<-5 Locus.Columns<- Loci*2 x<-seq(1,Locus.Columns,2) result<-matrix(8,8,Loci) for (i in 1:Loci){ for (j in 1:8){ for (k in x){ result[j,i] <- sum(P.genotype.sample[,k]==j & P.genotype.sample[,k+1]==j) } } } result # Below is a long a...

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus (e.g., "Locus1" or "Locus2", ... or "Locus6"), the individuals have either one allele (from the set of A,T,C,G) or one other allele (from the set of A,T,C, G). For example,...

...use my own labels. I was told my another well-versed R programmer to use the follow script: x<-as.matrix(test1[,-1]) ## skip column 1 rownames(x)<- test[1,] heatmap(x, scale="none") This was for data set up in 4 columns such as when you read the data in R it looks like: Loci Cont NaCl Peg 1 0231 2.1 4.2 4.1 2 1253 4.1 2.3 2.3 3 8167 5.7 1.1 3.4 Using the script above and this dataset it worked well - the Loci was used as the row labels rather than the numbers assigned by R. Looking at the data...

...obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci(). A piece from the dataset is displayed further below. Here my code: /Code/ library("ape") library("adegenet") library("pegas") / load with no problem. / /the command: / > data.loci <- read.loci(file ="/Users/victor/Documents/SIV_Compartment/data/pegas...

...r and each row an individual. Microsatellite genotypes are formatted differently. An example is below. Each row is an individual and each column is one allele from a single locus. From the below values L1 and L1.1 each give a copy of an allele for same locus. Occasionally values from different loci will have the same value altough these are not actually the same allele. I would like the calculation of the proportion of shared values for alleles to be restricted to the proportion of shared alleles within loci for all individuals (pairs of columns L1 and L1.1, L2 and L2.2....) What I have now...

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above would do 51 loci at a time. I want to do 600...

...s an object of type character? Thanks in advance, Neil Background ======== This is a refined example from a larger problem that I'm working on. Given a data frame of pairs of columns containing genotype data I would like to convert them to genotype objects using makeGenotypes. The number of loci (i.e. ncol() / 2) is variable, so I like to be able to determine how many loci there are and then convert all of them. Thus an example data set would be... <-----Start test.dat------> ID,rs1.1,rs1.2,rs2.1,rs2.2,rs3.1,rs3.2,rs4.1,rs4.2,rs5.1,rs5.2,rs6.1,rs6.2 A0001,1,1,1,2,1,1,2,2,1,2,1,1 A0...

Rers, I have been using the function 'by' in such a manner: by(LogMetric, list(Loci.Number=Loci.Number, Code.Flag=Code.Flag), plot) with par(mfrow=c(5,3)) to produce a single R Graphics: Device with 14 different plots on it as described above in my 'by' statement. Thank you for helping me thus far. A similar command using 'tapply' can be written as well. My...

...or list element have the same number of rows and create one large data.frame. # below is a creation of a sample list # I apologize for the length in creating the list it is the only way i could figure # out how to convey my puzzle. If you scroll down you will find it as " list.sample." Loci<-4 Pairwise<- (Loci*(Loci-1))/2 #Creation of list elements c1<- c(1,4,3,2,4,1,3,2,4,3) c2<- c(2,4,3,4,2,3,4,1,3,2) c3<- c(1,3,2,4,4,3,4,4,2,2) c4<- c(2,3,2,3,1,3,2,4,4,3) c5<- c(1,2,1,1,2,2,3,3,2,1) c6<- c(3,2,4,3,1,1,2,3,3,4) c7<- c(1,2,1,2,3,2,3,2,1,2) c8<- c(1,2,2...

Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency. What statistical test should I use? My table looks like Chromosome position Major/minor Resequencing SN...

I?m tryng to use the SPDEP package in my research in the field of population genetics. My data set has the following format: - x and y : coordinates, - Z: allelic frequency in each loci (in a total of 8 locis) - this variable can assume the values 0 ; 0.5 or 1. The objective is to verify if there is a possible spatial autocorrelation structure of the allelic frequency in a population of natives trees (copaifera langsdorffii). I had some doubts about the package: 1) Is the pac...

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other words one human, one row. If there were multiple loci then the variables would continue to be heaped up on the rig...

Hi everyone, I'm the developer of the Loci programming language ( http://loci-lang.org ), for which the compiler is a front-end for LLVM. I would like to say that LLVM has been extremely useful for the development of the compiler and so thank you everyone for building this amazing system. ---- Virtual Method Calls ---- While most aspects...

Hi, These are two problems I've never seen when I used xtable() before... R 1.9.1 for Windows XP, xtable version 1.2-3: > final.df Loci Chr Marker Position P.values Deviance DF 1 Idd5 1 D1Mit181 42.6 0.0011 103.21 78 2 Idd6/19/20 6 D6Mit374 66.7 0.0014 104.29 78 3 Idd13 2 D2Mit490 64.5 0.0025 97.83 78 4 Idd8/12 13 D14Mit109 24 0.0244 102.41 78 5...

Hello, I tried to align lines of text in the legend of a plot. It always defaults to the central alignment. How can I adjust it to be left alignment? Here is the code fragment written in python using Rpy module: text = 'Quantiles #Loci\n' text += '%s %6d\n' % (' 100',totalloci) text += '%s %6d\n' % (' 95',per95cntloci) text += '%s %6d\n' % (' 50',per50cntloci) r.legend(20,30,text,cex=0.6,bty='n') Thanks Zhaoming [[alternat...

I have a question about the "write.table" I have 100 data.frames, loci1, loci2, loci3.............,loci100. now, I want to print these data.frames to 100 separate files, and the names of the files are also loci1, loci2, loci3,......., loci100. how to perform this under a "for" loop? say, for (i in 1:100) { write.table(...., file='...', ........)...

Hi All, I am trying to plot outlier loci in R from data generated by BayesFst. The developers provide the code which I use but I can't seem to get it to work consistently. Sometimes I can get R to generate a plot (without confidence intervals or loci IDs) and other times I cannot even generate P-values using the code supplied. I am...

...#####zones####################################################### #ZONE TYPE OPTIONS IN OUT # OPTIONS OPTIONS fw firewall ############ Hardware Local Network ############## #local Network interface loci ipv4 #local network loc:loci desk1:loc ################################################ ############# Venet Local Network ############## #Virtual Interface venet ipv4 #Virtual network (see hosts file) ven1:venet #VPS servers web1:ven1 serv2:ven1 dmz:ven1 #LAST LINE - ADD YOUR ENTRIES...

On 1/21/13 5:22 AM, Alexandru Ionut Diaconescu wrote: > Hello everyone ! > > I am trying to determine for certain Load instructions from my pass > their corresponding Alloca instructions (that can be in other previous > blocks). The chain can be something like : `TargetLoad(var) -> other > stores/loads that use var (or dependencies on var) -> alloca(var).` , > linked

...ogic. Clang performs this encoding and indeed > > >> much > > >> of the current functionality is derived from Clang's source. > > >> > > >> This project originated as a necessary piece of functionality for > > >> the > > >> Loci compiler frontend [1] and is now an external dependency; my > > >> aim > > >> is to make this usable for other LLVM frontends that also need to > > >> generate ABI-compliant IR (I assume this is a fairly large subset > > >> of > > >> the f...