search for: geno

...ehaviours and 2) alleles between numerous individuals. Pasted below ('propshared' function) is what I have now and and works very well for calculating the proportion of shared behaviours where the data is formatted with each column as a behaviour 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 no...

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 package:...

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(run...

..., 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, -1, -1, 0, 1, 0, 0, 0, 2, 0, 1, 0, 0, 0, 2, 0, 1, 1, 2, 0, 0, 1, 0, 1, -1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 2, 0, 0, 0, 1, 1, 1, 0, 0 ) GENO <- matrix( g , nrow = n ,byrow=T) GENO[GENO == -1 ] <- NA? # Function library(ordinal) ???? Rplink <- function(PHENO,GENO,CLUSTER,COVAR) ???? { ????? f1 <- function(s) ????? { ??????? m <- summary(clm(PHENO ~ s)) ??????? r <- c(m$coef) ??????? c( length(r) , r ) ????? } ???? a...

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...

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 SNP markers. I wish to repeat this procedure multiple times (~1000) permuting the cases and controls (affection status). It seems straightforward to implement it like this: ###...

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=3...

...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 Consor...

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 as.character(levels(elemconc$regio...

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 tho...

...F20HET E11.5 F9.20DKO KTr3 E11.5 F9.20DKO KTr3 E11.5 F9.20DKO E11.5 F9.20DKO PEd2 E11.5 F9.20DKO PEd2 E11.5 F9.20DKO E11.5 F9.20DKO j0J1 E11.5 F9.20DKO j0J1 E11.5 F9.20DKO > colnames(samples) [1] "quant_samples" "age" "geno" Really, really confused. On Tue, Oct 24, 2017 at 12:58 PM, Ed Siefker <ebs15242 at gmail.com> wrote: > Why doesn't this work? > >> samples$geno <- as.data.frame(sapply(yo, toupper), col.names="geno") >> samples > quant_sa...

...ble 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 nested in sex. XY and YY individuals are males and WX and WY females. I crossed 8 XY males with 8 WY females and 8 YY males with 8 WX females. Each cross corresponds to a family (i.e. family 1 to 8 for XY x WY and family 9 to 16 for YY...

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

...1.22,1.34, 2.44, ...) z1<-data.frame(x,y) summary(glm(y1~x1,data=z1) But I do the same thing by inputting the data sets from the two files e <- read.table("file1.txt", header=TRUE,row.names=1) g <- read.table("file2.txt", header=TRUE,row.names=1) e1<-exp[1,] g1<-geno[1,] d1<-data.frame(g, e) summary(glm(e1 ~ g1, data=d1)) the error message is Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type Execution halted Thanks in advance, Ying [[alternative HTML version deleted]]

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) library(stats) modadd = glm(geno$casectrln ~rs743572_2 + factor(racegrp)+ factor(smokgp)+ factor(alcgp)+ factor(bmigp) + factor(ipssgp) +...

..., this even though I use the default setting NA in my 'score matrix'. I am therefore trying to enter a matrix of 103 x 9 (103 individual x 9loci) with 0 for real alleles (null or not) and 1 for non scored alleles called upon using the miss.loc function in MCMC, in addition to the 'genotype' and 'coordinate' matrices. However when starting the MCMC, after initialisation of all functions I get this message: list (object) can not be coerced into integer And the MCMC is stopped. I only get this message when entering the 'null allele' matrix and using the m...

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 inter...