inst/scripts/rebuildDatasets.R

In samWieczorek/DAPARdata: Data accompanying the DAPAR and Prostar packages

Set_X_CC_infos <- function(obj){
  Xshared <- BuildAdjacencyMatrix(obj, "Protein_group_IDs", FALSE)
  Xunique <- BuildAdjacencyMatrix(obj, "Protein_group_IDs", TRUE)
  ll.X <- list(matWithSharedPeptides = Xshared, 
               matWithUniquePeptides = Xunique)
  obj <- SetMatAdj(obj, ll.X)
  ll1 <- get.pep.prot.cc(GetMatAdj(obj)$matWithSharedPeptides)
  ll2 <- DAPAR::get.pep.prot.cc(GetMatAdj(obj)$matWithUniquePeptides)
  cc <- list(allPep = ll1, 
             onlyUniquePep = ll2)
  obj <- SetCC(obj, cc)
  
  return(obj)
}


source(file = 'Exp1_R2_pept.R')
save(Exp1_R2_pept, file = '../../data/Exp1_R2_pept.RData')
saveRDS(Exp1_R2_pept, '../extdata/Exp1_R2_pept.MSnset')

source(file = 'Exp1_R2_prot.R')
save(Exp1_R2_prot, file = '../../data/Exp1_R2_prot.RData')
saveRDS(Exp1_R2_prot, '../extdata/Exp1_R2_prot.MSnset')

source(file = 'Exp1_R25_pept.R')
save(Exp1_R25_pept, file = '../../data/Exp1_R25_pept.RData')
saveRDS(Exp1_R25_pept, '../extdata/Exp1_R25_pept.MSnset')

source(file = 'Exp1_R25_prot.R')
save(Exp1_R25_prot, file = '../../data/Exp1_R25_prot.RData')
saveRDS(Exp1_R25_prot, '../extdata/Exp1_R25_prot.MSnset')

source(file = 'Exp2_R2_pept.R')
save(Exp2_R2_pept, file = '../../data/Exp2_R2_pept.RData')
saveRDS(Exp2_R2_pept, '../extdata/Exp2_R2_pept.MSnset')

source(file = 'Exp2_R2_prot.R')
save(Exp2_R2_prot, file = '../../data/Exp2_R2_prot.RData')
saveRDS(Exp2_R2_prot, '../extdata/Exp2_R2_prot.MSnset')

source(file = 'Exp2_R10_pept.R')
save(Exp2_R10_pept, file = '../../data/Exp2_R10_pept.RData')
saveRDS(Exp2_R10_pept, '../extdata/Exp2_R10_pept.MSnset')

source(file = 'Exp2_R10_prot.R')
save(Exp2_R10_prot, file = '../../data/Exp2_R10_prot.RData')
saveRDS(Exp2_R10_prot, '../extdata/Exp2_R10_prot.MSnset')

source(file = 'Exp2_R100_pept.R')
save(Exp2_R100_pept, file = '../../data/Exp2_R100_pept.RData')
saveRDS(Exp2_R100_pept, '../extdata/Exp2_R100_pept.MSnset')

source(file = 'Exp2_R100_prot.R')
save(Exp2_R100_prot, file = '../../data/Exp2_R100_prot.RData')
saveRDS(Exp2_R100_prot, '../extdata/Exp2_R100_prot.MSnset')