search for: effectors

Hi, I have some values in a list format generated by the following: Path_Number <- 0010 ID.Path <- formatC(0001:Path_Number, width=4, flag=0) # Make vector of ID's. No_of_Effectors <- sample(1:550, length(ID.Path), replace=TRUE) # Define Number of Effectors each individual gets. Effectors <- split(sample(1:10000, sum(No_of_Effectors), replace=TRUE), rep(ID.Path, No_of_Effectors)) # Generate effectors and dish them out. Effectors And I've written a chunk which is de...

...operated on, before being stored again in the dataframes. Below is how I've created my dataframe and stored my effector genes. In this model, effector genes are numerical values between 1 and 10000. Path_Number <- 0500 inds <- data.frame(ID=formatC(0001:Path_Number,width=4,flag=0),No_of_Effectors="",No_Expressed_Effectors="") inds$No_of_Effectors <- round(as.numeric(lapply(1:nrow(inds),function(x) runif(1, min=1, max=550)))) Effectors <- lapply(1:nrow(inds),function(x) sample(1:10000,inds$No_of_Effectors,replace=TRUE)) inds <- data.frame(inds,Effectors=as.charac...

Hi All, I'm trying to run a simulation of host-pathogen evolution based around individuals. What I need to have is a dataframe or table of some description - describing all the individuals of a pathogen population (so far I've implemented this as a matrix): ID No_of_Effectors Effectors (Sequences) [1,] 0001 3 ## 3 Random Numbers ## There will be many such rows for many individuals. They have something called effectors, the number of which is randomly generated, so say you get 3 in the No_of_Effectors column. Then I m...

...ulation I'm building: Mutate<-function(x){ l<-0 for(i in x){ l2<-0 l<-l+1 for(i in x[[l]]){ l2<-l2+1 if(runif(1) < 0.9) ifelse(runif(1) <0.5, x[[l]][l2] <- x[[l]][l2]+1, x[[l]][l2] <- x[[l]][l2]-1) } } return(x) } I call this with Effectors<-Mutate(X) The function is designed to alter the values of each element in X by either + or - 1 (50:50 chance wether + or -). However Y, elements of which are a subset of the corresponding elements of X, need to be consistent i.e. if a value in X is changed, and that value is part of the Y subse...

I use the step() function occasionally, and I think I understand its objective, proper use, and limitations. Now I see stepwise model selection being used in what seems to be an unusual way, and I wonder if it is right or wrong. May I describe? Genetic mapping tries to find where in an animal's genome are genetic elements that influence a particular physical trait. Say there are 100

Hi All, Can anyone suggest how to make rsync work in order to replicate double-byte characters ? Thanks to anyone who can help aslay

...nl/vacancies.php) THREE BIOINFORMATICS POSITIONS PROJECT OUTLINE Genomic alterations are major determinant of responses to (targeted) therapies in cancer. In fact, the best positive and negative predictors of responses to targeted therapies are alterations in kinases or their direct downstream effectors. To gain insight into resistance mechanisms to therapy and thus better tailor treatment, we are approaching this problem from two different angles. First, we have acquired large panels of human tumors, on which we are currently performing kinase exon sequencing. More specifically, we are performing...