nci60-drugtox: NCI-60 Drug Toxicity Data

library(dplyr)
library(reshape2)

load("data/cells.rda")

src <- "http://discover.nci.nih.gov/cellminerdata/rawdata/DTP_NCI60_RAW.zip"
lcl <- "data-raw/DTP_NCI60_RAW.zip"
if (!file.exists(lcl)) {
    download.file(src, lcl)
}

headers = c("NSC.id","drug","FDA.status","mechanism","pubchem",
            "total.probes","total.after.quality.control", "failure.reason",
            "experiment","BR.MCF7","BR.MDA_MB_231","BR.HS578T","BR.BT_549",
            "BR.T47D","CNS.SF_268","CNS.SF_295","CNS.SF_539","CNS.SNB_19",
            "CNS.SNB_75", "CNS.U251","CO.COLO205","CO.HCC_2998","CO.HCT_116",
            "CO.HCT_15","CO.HT29","CO.KM12","CO.SW_620","LE.CCRF_CEM",
            "LE.HL_60","LE.K_562","LE.MOLT_4","LE.RPMI_8226","LE.SR",
            "ME.LOXIMVI","ME.MALME_3M","ME.M14","ME.SK_MEL_2","ME.SK_MEL_28",
            "ME.SK_MEL_5","ME.UACC_257","ME.UACC_62","ME.MDA_MB_435","ME.MDA_N",
            "LC.A549","LC.EKVX","LC.HOP_62","LC.HOP_92","LC.NCI_H226",
            "LC.NCI_H23","LC.NCI_H322M","LC.NCI_H460","LC.NCI_H522","OV.IGROV1",
            "OV.OVCAR_3","OV.OVCAR_4","OV.OVCAR_5","OV.OVCAR_8","OV.SK_OV_3",
            "OV.NCI_ADR_RES","PR.PC_3","PR.DU_145","RE.786_0","RE.A498",
            "RE.ACHN","RE.CAKI_1","RE.RXF_393","RE.SN12C","RE.TK_10",
            "X")

nci60.drugs <- read.delim2(unz(lcl, "DTP_NCI60_RAW.txt"),skip=8)
names(nci60.drugs) <- headers
nci60.drugs <- nci60.drugs %>% select(-X)
save(nci60.drugs, file="data/nci60drugs.rda")

df <- melt(nci60.drugs, id.vars = c("NSC.id","drug","pubchem","experiment"),
           value.name = "toxicity", 
            measure.vars = c("BR.MCF7","BR.MDA_MB_231","BR.HS578T","BR.BT_549",
            "BR.T47D","CNS.SF_268","CNS.SF_295","CNS.SF_539","CNS.SNB_19",
            "CNS.SNB_75", "CNS.U251","CO.COLO205","CO.HCC_2998","CO.HCT_116",
            "CO.HCT_15","CO.HT29","CO.KM12","CO.SW_620","LE.CCRF_CEM",
            "LE.HL_60","LE.K_562","LE.MOLT_4","LE.RPMI_8226","LE.SR",
            "ME.LOXIMVI","ME.MALME_3M","ME.M14","ME.SK_MEL_2","ME.SK_MEL_28",
            "ME.SK_MEL_5","ME.UACC_257","ME.UACC_62","ME.MDA_MB_435","ME.MDA_N",
            "LC.A549","LC.EKVX","LC.HOP_62","LC.HOP_92","LC.NCI_H226",
            "LC.NCI_H23","LC.NCI_H322M","LC.NCI_H460","LC.NCI_H522","OV.IGROV1",
            "OV.OVCAR_3","OV.OVCAR_4","OV.OVCAR_5","OV.OVCAR_8","OV.SK_OV_3",
            "OV.NCI_ADR_RES","PR.PC_3","PR.DU_145","RE.786_0","RE.A498",
            "RE.ACHN","RE.CAKI_1","RE.RXF_393","RE.SN12C","RE.TK_10"))

#remove NAs and trun Toxicity into numeric
names(df)[names(df) == "variable"] <- "cell.line"
df <- df %>% filter(toxicity != "na")
df$toxicity <- as.numeric(df$toxicity)
df <- df %>% left_join(cells,by="cell.line")
nci60 <- df

nci60 <- nci60 %>% select(NSC.id,drug, pubchem, cell.line, toxicity, 
                          tissue, age, sex, prior.treatment, epithelial, 
                          histology, source, ploidy,p53, mdr, doubling.time,
                          institute)

save(nci60, file="data/nci60.rda")

#drugdata <- nci60.drugs %>% select(NSC.id,Drug.name,FDA.status,Mechanism.of.action,PubChem.id)