search for: effector

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 d...

Hi, First my apologies for a non-working piece of code in a previous submission, I have corrected this error. I'm doing is individual based modelling of a pathogen and it's host. The way I've thought of doing this is with two dataframes, one of the pathogen and it's genes and effector genes, and one of the host and it's resistance genes. During the simulation, these things can be pulled out of the dataframes and 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...

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...

...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 subs...

...sts to then treat the results of the stepwise model selection as yet a fourth analytical tool by which to rank all the mapping markers, i.e., as further evidence that a marker must be near a genetic element affecting the trait. "If it's included in the model, it must be close to a genetic effector of the trait". How does this sound to you? If a stepwise algorithm ranks possible cofactors--perhaps even assigns them an F value--can you use that ranking to make any comparisons among possible cofactors? What do the F values mean? **********************************************************...

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 performin...