Ecological Genomics GWAS point of view

Long term Goals Data conversation between different popular software in the field Develop scripts to qualitatively filter data using R

Flow

What is done from the flow 2 filter scripts 1 st describes the data – f1<-apply(apply(f,2,is.na),2,sum) #Counts number of missing values – hist(f1) #And creates a plot – hist(colMeans(f5,na.rm=T)) #Calculates allele freq distribution

What is done from the flow Filtering step 1 hist(f1)f1<-apply(apply(f,2,is.na),2,sum) hist(colMeans(f5,na.rm=T))

Once user evaluates the data and decides on the selection of markers/phenotypes. – drop.col.kna <- function(mydf, l) mydf[sapply(mydf, function(x) sum(is.na(x))) < l] f1<-drop.col.kna(mydf, l) What is done from the flow Filtering step 2

What is done from the flow PCA PCA using princomp function – write.table(pca$loading) # summarizes variance of each of the components/eigenvectors – Plot(pca) # visualizes the amount of the variance that is explained by the principal components – Write.table(Summary(pca)) # standard pca output (What is the variance that each component contributes) – Write.table(Pca$scores) #contribution of each sample in the total variance of each of the eigenvectors – Biplot(pca) & plot of the pca

What is done from the flow pca Write.table(pca$loadings) plot(pca) Write.table(summary(pca)) Write.table(pca$scores)

PCA plots

What is done from the flow Structure Structure is already installed and evaluated by me, Nicole Input and parametersoutput

What is done from the flow PGDSpider

PGDSpider Documentation needs polishing New version was installed and deployed needs to be tested

Next 2 months Add an R script to perform mantel test for Isolation by distance Fix the PCA due to a bug for missing data Create workflows: – Link the VCF data format via PGDSpider with Structure – Link the filtering scripts with PCA script for the Phenotypic analysis