data-raw/import_raw_data.R

In VoisinneG/InteRact: Analysis of affinity purification/tandem MS data

# import_KEGG_pathway_info <- function( dest_dir="~/ownCloud//++Work/++Research/Resources-Databases/KEGG/", organism="mouse"){
#   
#   url_adres <- switch(organism,
#                       "mouse" = "http://rest.kegg.jp/link/mmu/pathway",
#                       "human" = "http://rest.kegg.jp/link/hsa/pathway")
#   
#   file_name <- switch(organism,
#                       "mouse" = "KEGG_mmu.txt",
#                       "human" = "KEGG_hsa.txt")
#   
#   dest_file <- paste(dest_dir, file_name, sep="")
#   
#   if(!file.exists(dest_file)){
#     download.file(url_adres, destfile = dest_file)
#   }
#   
#   KEGG <- read.table(dest_file, header=FALSE)
#   names(KEGG) <- c("pathway", "id")
#   
#   u_pathway <- unique(KEGG$pathway)
#   name_pathway <- rep("", length(u_pathway))
#   gene_pathway <- rep("", length(u_pathway))
#   
#   for ( i in 1:length(u_pathway) ){
#     
#     gene_pathway[i] <- paste(as.character(KEGG$id[which(KEGG$pathway == u_pathway[i])]), collapse=";")
#     
#     #for ( i in 1:100 ){
#     url_adres <- paste("http://rest.kegg.jp/get/", u_pathway[i],sep="")
#     dest_file <- paste("~/ownCloud/++Work/++Research/Resources-Databases/KEGG/",u_pathway[i],".txt")
#     if(!file.exists(dest_file)){
#       download.file(url_adres, destfile = dest_file)
#     }
#     KEGG_pthw <- readLines(dest_file)
#     s <- strsplit(KEGG_pthw[2], split = " ")[[1]]
#     s <- s[s!=""]
#     name_pathway[i] <- paste(s[2:(which(s=="-")-1)], collapse=" ")
#   }
#   
#   df <- data.frame(pathway = u_pathway, name = name_pathway, IDs = gene_pathway)
#   
#   return(df)
# }
# 
# KEGG_mouse <- import_KEGG_pathway_info(organism="mouse")
# 
# KEGG_human <- import_KEGG_pathway_info(organism="human")
# 
# # # import uniprot data ------------------------------------------------------------------------------------------
# 
# uniprot_data_mouse <- read.table( paste("~/ownCloud/++Work/++Research/Resources-Databases/",
#                                         "Uniprot/uniprot-mus+musculus.txt", sep=""),
#                                   sep="\t", header=TRUE, fill=TRUE, quote=c("\""),comment.char="")
# 
# # Note that only reviewd human protein are imported
# 
# uniprot_data_human <- read.table( paste("~/ownCloud/++Work/++Research/Resources-Databases/",
#                                         "Uniprot/uniprot-homo+sapiens+AND+reviewed.txt", sep=""),
#                                   sep="\t", header=TRUE, fill=TRUE, quote=c("\""),comment.char="")
# 
# # import Reactome data ------------------------------------------------------------------------------------------
# 
# reactome <- read.table( paste("~/ownCloud/++Work/++Research/Resources-Databases/Reactome/",
#                               "UniProt2Reactome_All_Levels.txt", sep=""),
#                         sep="\t", header=FALSE, fill=TRUE, quote=c("\""),comment.char="", as.is=TRUE)
# 
# names(reactome) <- c("Protein.ID", "ID", "link", "Name", "Type", "Organism")
# 
# reactome_mouse <- reactome[ which(reactome$Organism == "Mus musculus"), ]
# 
# reactome_human <- reactome[ which(reactome$Organism == "Homo sapiens"), ]
# 
# # import PFAM data ----------------------------------------------------------------------------------------------
# 
# pfam_mouse <- read.table( paste("~/ownCloud/++Work/++Research/Resources-Databases/PFAM/",
#                                 "10090.tsv", sep=""),
#                           sep="\t", header=FALSE, skip=3, fill=TRUE, quote=c("\""),comment.char="", as.is=TRUE)
# names(pfam_mouse) <- c("seq id",
#                        "alignment.start",
#                        "alignment.end",
#                        "envelope.start",
#                        "envelope.end",
#                        "hmm.acc",
#                        "hmm.name",
#                        "type",
#                        "hmm.start",
#                        "hmm.end",
#                        "hmm.length",
#                        "bit.score",
#                        "E.value",
#                        "clan")
# 
# pfam_human <- read.table( paste("~/ownCloud/++Work/++Research/Resources-Databases/PFAM/",
#                                 "9606.tsv", sep=""),
#                           sep="\t", header=FALSE, skip=3, fill=TRUE, quote=c("\""),comment.char="", as.is=TRUE)
# 
# names(pfam_human) <- names(pfam_mouse)
# 
# # import Hallmark data ------------------------------------------------------------------------------------------
# 
# Hallmark_input <- readLines("~/ownCloud/++Work/++Research/Resources-Databases/Hallmark_database/h.all.v6.1.symbols.gmt.txt")
# Hallmark_split <- strsplit(Hallmark_input, split="\t")
# 
# Hallmark_name <- rep("", length(Hallmark_split))
# Hallmark_genes <- rep("", length(Hallmark_split))
# 
# for ( i in 1:length(Hallmark_split) ){
#   Hallmark_name[i] <- Hallmark_split[[i]][1]
#   Hallmark_genes[i] <- paste(Hallmark_split[[i]][3:length( Hallmark_split[[i]] )], collapse=";")
# }
# 
# Hallmark <- data.frame(name = Hallmark_name,  gene = Hallmark_genes)
# 
# 
# # import GO data -----------------------------------------------------------------------------------------------
# 
# library("ontologyIndex")
# 
# onto <- get_ontology("~/ownCloud/++Work/++Research/Resources-Databases/GO/go.obo", propagate_relationships = "is_a",
#                      extract_tags = "everything")
# 
# names_gaf <- c(
#   "DB",
#   "DB_Object_ID",
#   "DB_Object_Symbol",
#   "Qualifier",
#   "GO_ID",
#   "DB:Reference",
#   "Evidence Code",
#   "With (or) From",
#   "Aspect",
#   "DB_Object_Name",
#   "DB_Object_Synonym",
#   "DB_Object_Type",
#   "Taxon and Interacting taxon",
#   "Date",
#   "Assigned_By",
#   "Annotation_Extension",
#   "Gene_Product_Form_ID"
# )
# 
# #Import GOA annotations for mouse uniprot proteome
# GOA_mouse <- read.table("~/ownCloud/++Work/++Research/Resources-Databases/GO/goa_mouse.gaf", sep="\t", skip=12, quote="\"")
# 
# names(GOA_mouse) <- names_gaf
# idx_match <- match(GOA_mouse$GO_ID, onto$id)
# GOA_mouse$GO_type <- onto$namespace[idx_match]
# GOA_mouse$GO_name <- onto$name[idx_match]
# 
# #Import GOA_slim annotations for mouse uniprot proteome
# GOA_mouse_slim <- read.table("~/ownCloud/++Work/++Research/Resources-Databases/GO/goa_mouse_mapped_to_goslim_generic.gaf", sep="\t", skip=12, quote="\"")
# 
# names(GOA_mouse_slim) <- names_gaf
# idx_match <- match(GOA_mouse_slim$GO_ID, onto$id)
# GOA_mouse_slim$GO_type <- onto$namespace[idx_match]
# GOA_mouse_slim$GO_name <- onto$name[idx_match]
# 
# #Import GOA annotations for mouse uniprot proteome
# GOA_human <- read.table("~/ownCloud/++Work/++Research/Resources-Databases/GO/goa_human.gaf", sep="\t", skip=12, quote="\"")
# 
# names(GOA_human) <- names_gaf
# idx_match <- match(GOA_human$GO_ID, onto$id)
# GOA_human$GO_type <- onto$namespace[idx_match]
# GOA_human$GO_name <- onto$name[idx_match]
# 
# #Import GOA_slim annotations for mouse uniprot proteome
# GOA_human_slim <- read.table("~/ownCloud/++Work/++Research/Resources-Databases/GO/goa_human_mapped_to_goslim_generic.gaf", sep="\t", skip=12, quote="\"")
# 
# names(GOA_human_slim) <- names_gaf
# idx_match <- match(GOA_human_slim$GO_ID, onto$id)
# GOA_human_slim$GO_type <- onto$namespace[idx_match]
# GOA_human_slim$GO_name <- onto$name[idx_match]



# import HPRD database

#THPRD <- read.table(paste("~/ownCloud/++Work/++Research/Resources-Databases/HPRD/",
                    #       "HPRD_Release9_062910/BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt",
                    #       sep=""),
                    # sep="\t",header = TRUE,quote="\"")

# import proteome data ------------------------------------------------------------------------------------------

# load("~/ownCloud/++Work/++Research/++Projects/Proteomes/Merge_Proteome_OST_and_CD4_kinetics/proteome_CD4.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Proteomes/Proteome_CD4+_transfected_expanded/proteome_CD4_expanded.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Proteomes/Proteome_Jurkat_Itsn2_KO/proteome_Jurkat.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Cbl.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Cblb.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Fyb.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Grb2.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Inpp5d.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Itk.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Lck.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Lcp2.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Nck1.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Nfatc2.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Plcg1.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Ptpn22.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Ptpn6.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Themis.rda")
# load("~/ownCloud/++Work/++Research/++Projects/Integration_16_interactomes/Analysis/InteRactomes/Interactome_Vav1.rda")

# proteome_data <- read.table(paste("~/ownCloud/++Work/++Research/++Projects/",
#                                   "Proteomes/Proteome_Comparison_OST_vs_kinetics/",
#                                   "Copy_number_hist_all_aligned_short.txt",
#                                   sep="" ),
#                             sep="\t",header=TRUE)




# save in ./R/sysdata.rda  ---------------------------------------------------------------------------------------

#devtools::use_data(
  #uniprot_data_mouse,
  #uniprot_data_human,
  #reactome_mouse,
  #reactome_human,
  #pfam_mouse,
  #pfam_human,
  #KEGG_mouse,
  #KEGG_human,
  #Hallmark,
  #GOA_mouse,
  #GOA_mouse_slim,
  #GOA_human,
  #GOA_human_slim,
  #proteome_CD4,
  #proteome_CD4_expanded,
  #proteome_Jurkat,
  #THPRD,
  #pkg=".",
  #internal = TRUE,
  #overwrite = TRUE)

# devtools::use_data( uniprot_data_mouse,
#                     #uniprot_data_human,
#                     proteome_data,
#                     pkg=".",
#                     internal = TRUE,
#                     overwrite = TRUE)

library(InteRact)
library(readxl)

proteinGroups_Cbl <- read.csv("~/extra/ProteinGroups_Cbl.txt", sep="\t", nrows=-1, fill=TRUE, na.strings="", dec=",")

conditions <- identify_conditions(proteinGroups_Cbl)
conditions$bckg <- gsub("Cbl", "CBL-OST", conditions$bckg)
conditions$bckg <- gsub("WT", "Wild-type", conditions$bckg)
conditions$time <- paste("t=", conditions$time, "s", sep = "")
conditions$bio <- gsub("Ech", "Sample ", conditions$bio)
conditions$tech <- gsub("R", "Injection  ", conditions$tech)
names(conditions) <- c("name", "bait", "Cell.type",  "Stim.time", "Bio.rep", "Tech.rep")

dir.create("./inst/")
dir.create("./inst/extdata/")
write.csv(conditions, file = "./inst/extdata/proteinGroups_Cbl_metadata.csv", row.names = FALSE, quote = FALSE)


res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl")
res <- identify_interactors(res, p_val_thresh = 0.05, fold_change_thresh = 2)
Interactome_Cbl <- res

usethis::use_data(proteinGroups_Cbl,
                  Interactome_Cbl,
                   # proteome_CD4,
                   # proteome_CD4_expanded,
                   # proteome_Jurkat,
                   # Interactome_Cbl,
                   # Interactome_Cblb,
                   # Interactome_Fyb,
                   # Interactome_Grb2,
                   # Interactome_Inpp5d,
                   # Interactome_Itk,
                   # Interactome_Lck,
                   # Interactome_Lcp2,
                   # Interactome_Nck1,
                   # Interactome_Nfatc2,
                   # Interactome_Plcg1,
                   # Interactome_Ptpn22,
                   # Interactome_Ptpn6,
                   # Interactome_Themis,
                   # Interactome_Vav1,
                   #pkg=".",
                   internal = FALSE,
                   overwrite = TRUE)