search for: genos

...oportion of shared values for alleles across loci. A specific example is that I would like the value *2* for individual *w *at * L1* to be considered the same as the value* 2* for individual *y* at *L1.1*but not the same as the value *2* for any other individual within any other pair of columns. genos<- data.frame( L1 = c(2,NA,1,3), L1 = c(1,NA,2,3), L2 = c(5,2,5,3), L2 = c(3,4,2,4), L3 = c(4,5,7,2), L3 = c(4,6,6,6) ) rownames(genos) = c("w","x","y","z") > genos L1 L1.1 L2 L2.1 L3 L3.1 w 2 1 5 3...

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required

Hi, I've tried to update my samba AD/DC environment. Then, I've removed a existing offline DC with "samba-tool domain demote --remove-other-dead-server=genos". I've re-created "genos" (yes, I try to keep the same name and IP address) and install a 4.10.2 samba version (I know the new version is 4.11.0). When I've tried to join it on my domain, I've received message "Join failed - cleaning up" and the error ERROR(runt...

Hi, ? I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's

I'm sorry to I forgot answer appropriate. I'm running CentOS 7 with all packages upgraded. I've followed instruction in https://wiki.samba.org/index.php/Package_Dependencies_Required_to_Build_Samba with some need modifications (yum line is bellow this text) and I've installed python 3.4. I've installed Bind9 from package manager where Bind9 version is 9.9.4. YUM command to

On 11/10/2019 21:56, Igor Sousa via samba wrote: > Hi, > > I've tried to update my samba AD/DC environment. Then, I've removed a > existing offline DC with "samba-tool domain demote > --remove-other-dead-server=genos". I've re-created "genos" (yes, I try to > keep the same name and IP address) and install a 4.10.2 samba version (I > know the new version is 4.11.0). When I've tried to join it on my domain, > I've received message "Join failed - cleaning up" and the e...

Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3. Gene[Gene=="GG"]<-3 It always give me: Warning in `[<-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu

Hi everyone, I'm using the function 'HWE.exact' of 'genetics' package to compute p-values of the HWE test. My data set consists of ~600 subjects (cases and controls) typed at ~ 10K SNP markers; the test is applied separately to cases and controls. The genotypes are stored in a list of 'genotype' objects, all.geno, and p-values are calculated inside the loop over all

Why doesn't this work? > samples$geno <- as.data.frame(sapply(yo, toupper), col.names="geno") > samples quant_samples age sapply(yo, toupper) E11.5 F20het BA40 E11.5 F20het BA40 E11.5 F20HET E11.5 F20het BA45 E11.5 F20het BA45 E11.5 F20HET

Hello, When I try: geno <-read.table("2500.geno.tab",header=TRUE,sep="\t",na.strings=".",quote=" ",comment.char="",colClasses=c("factor"),nrows=2501) I get, after hour(s) of work: Error: cannot allocate vector of size 9 Kb I have: Rgui.exe --max-mem-size=3Gb and multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft

...when it said "/etc/named.conf:59: open: /usr/local/samba/bind-dns/named.conf: permission denied". The file exists and I've tired to change permissions of this file to own to root:named, but journalctl -xe still shows the same error. [root at newdc ~]# journalctl -xe Apr 17 14:11:19 genos named[5041]: built with '--build=x86_64-redhat-linux-gnu' '--host=x86_64-redhat-linux-gnu' '--program-prefi Apr 17 14:11:19 genos named[5041]: ---------------------------------------------------- Apr 17 14:11:19 genos named[5041]: BIND 9 is maintained by Internet Systems Consort...

I am trying to do this, but it won't work: > library(lattice) > elemconc = data.frame(expand.grid(id=1:20, geno=c('exp', 'wt'), region=c('cor', 'cr', 'spine'), elem=c('fe', 'cu', 'zn')), conc=rnorm(360, 10)) > elemconc$geno = factor(elemconc$geno) > elemconc$region = factor(elemconc$region) > for (i in

Hi all, Here is my problem: I performed bioassays using a unique insecticide on 9 different genotypes and got their mortality depending on the dose of insecticide used. Now, I want to see wether some genotypes are different or not in their responses to insecticide. My problem is that I have up to four replicates for some genotypes, but only one for other... Due to this unbalanced design, I

Wait. Now I'm really confused. > > head(samples) quant_samples age sapply(yo, toupper) E11.5 F20het BA40 E11.5 F20het BA40 E11.5 F20HET E11.5 F20het BA45 E11.5 F20het BA45 E11.5 F20HET E11.5 F20het BB84 E11.5 F20het BB84 E11.5 F20HET E11.5 F9.20DKO KTr3 E11.5 F9.20DKO KTr3 E11.5 F9.20DKO E11.5

Dear R Users, I am having trouble with lmer. I am looking at recombinant versus non recombinant individuals. In the response variable recombinant individuals are coded as 1's and non-recombinant as 0's. I built a model with 2 fixed factors and 1 random effect. Sex (males/females) is the first fixed effect and sexual genotype (XY, YY, WX and WY) the second one. Sexual Genotype is

I have data I'd like to plot using the formula interface to boxplot. I call boxplot like so: with(mydata, boxplot(count ~ geno * tissue)) I get a boxplot with x axis labels like "wt.kidney". I would like to change the '.' to a newline. Where is this separator configured? Thanks, -Ed

I have two data sets: File1.txt: Name id1 id2 id3 ... N1 0 1 0 ... N2 0 1 1 ... N3 1 1 -1 ... ... File2.txt: Group id1 id2 id3 ... G1 1.22 1.34 2.44 ... G2 2.33 2.56 2.56 ... G3 1.56 1.99 1.46 ... ... I like to do: x1<-c(0,1,0,...) y1<-c(1.22,1.34, 2.44, ...)

This will probably seem very simple to experienced R programmers: I am doing a snp association analysis and am at the model-fitting stage. I am using the Stats package's "drop1" with the following code: ##geno is the dataset ## the dependent variable (casectrln) is dichotomous and coded 0,1 ## rs743572_2 is one of the snps (which is coded 0,1,2 for the 3 genotypes)

I am trying to use the function 'filter.NA=TRUE' in Geneland. The function appears to be set on TRUE by default, as it appears as TRUE in the 'parameter.txt' file output and hence I do not need to enter the function per se (as it is an 'Unused argument otherwise') . Hence all my missing data (individuals that I have not yet scored at that specific loci) are scored as

mybp <- boxplot(count ~ geno * tissue, data = mydata, plot = FALSE) mybp$names <- gsub("\\.", "\n", mybp$names) bxp(mybp) See ?boxplot for details. Best, Ista On Thu, Sep 28, 2017 at 12:40 PM, Ed Siefker <ebs15242 at gmail.com> wrote: > I have data I'd like to plot using the formula interface to boxplot. > I call boxplot like so: > > with(mydata,