### R code from vignette source 'vignettes/SpacePAC/inst/doc/SpacePAC.Rnw' ################################################### ### code chunk number 1: Example1 ################################################### library(SpacePAC) ##Extract the data from a CIF file and match it up with the canonical protein sequence. #Here we use the 2ENQ structure from the PDB, which corresponds to the PIK3CA protein. CIF <- "http://www.pdb.org/pdb/files/2ENQ.cif" Fasta <- "http://www.uniprot.org/uniprot/P42336.fasta" PIK3CA.Positions <- get.AlignedPositions(CIF, Fasta, "A") ##Load the mutational data for PIK3CA. Here the mutational data was obtained from the ##COSMIC database (version 58). data(PIK3CA.Mutations) ##Identify and report the clusters. my.clusters <- SpaceClust(PIK3CA.Mutations, PIK3CA.Positions$Positions, numsims =1000, simMaxSpheres = 3, radii.vector = c(1,2,3,4), method = "SimMax") my.clusters ################################################### ### code chunk number 2: Example2 ################################################### ##Extract the data from a CIF file and match it up with the canonical protein sequence. #Here we use the 2ENQ structure from the PDB, which corresponds to the PIK3CA protein. CIF <- "http://www.pdb.org/pdb/files/3GFT.cif" Fasta <- "http://www.uniprot.org/uniprot/P01116-2.fasta" KRAS.Positions <- get.Positions(CIF, Fasta, "A") data(KRAS.Mutations) ##Identify and report the clusters. my.clusters <- SpaceClust(KRAS.Mutations, KRAS.Positions$Positions, radii.vector = c(1,2,3,4), alpha = .05, method = "Poisson") my.clusters ################################################### ### code chunk number 3: Example3 ################################################### ##To avoid RGL errors, this code is not run. However it has been tested and verified. #library(rgl) #CIF <- "http://www.pdb.org/pdb/files/3GFT.cif" #Fasta <- "http://www.uniprot.org/uniprot/P01116-2.fasta" #KRAS.Positions <- get.Positions(CIF, Fasta, "A") #make.3D.Sphere(KRAS.Positions$Positions, 12, 3)