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TCGA LUAD Normalized.R
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query <- GDCquery(project = "TCGA-LUAD",
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "normalized_results",
experimental.strategy = "RNA-Seq",
barcode = c("TCGA-05-4398",
"TCGA-05-4402",
"TCGA-05-4426",
"TCGA-35-4122",
"TCGA-38-4626",
"TCGA-38-6178",
"TCGA-44-2659",
"TCGA-44-3917",
"TCGA-44-6145",
"TCGA-44-6146",
"TCGA-44-6775",
"TCGA-44-7662",
"TCGA-44-7671",
"TCGA-44-A479",
"TCGA-49-AARN",
"TCGA-49-AARQ",
"TCGA-50-8459",
"TCGA-55-6983",
"TCGA-55-7903",
"TCGA-55-7907",
"TCGA-55-8094",
"TCGA-55-8299",
"TCGA-55-8511",
"TCGA-55-8513",
"TCGA-55-A48Y",
"TCGA-62-A472",
"TCGA-64-1681",
"TCGA-67-3770",
"TCGA-69-7760",
"TCGA-69-7974",
"TCGA-69-7980",
"TCGA-73-4658",
"TCGA-75-5125",
"TCGA-75-7030",
"TCGA-78-7150",
"TCGA-78-7154",
"TCGA-78-7158",
"TCGA-78-7537",
"TCGA-78-7542",
"TCGA-78-8648",
"TCGA-80-5611",
"TCGA-86-7953",
"TCGA-86-7955",
"TCGA-91-6829",
"TCGA-91-6836",
"TCGA-91-A4BC",
"TCGA-91-A4BD",
"TCGA-95-A4VK",
"TCGA-97-7554",
"TCGA-MP-A4TI",
"TCGA-MP-A4TJ",
"TCGA-NJ-A4YF",
"TCGA-05-4389",
"TCGA-05-4410",
"TCGA-05-4415",
"TCGA-05-4433",
"TCGA-05-5429",
"TCGA-38-4632",
"TCGA-44-5643",
"TCGA-44-5645",
"TCGA-44-6148",
"TCGA-44-A47B",
"TCGA-49-4488",
"TCGA-49-4510",
"TCGA-49-6742",
"TCGA-49-6767",
"TCGA-49-AAQV",
"TCGA-49-AARR",
"TCGA-50-5068",
"TCGA-50-5932",
"TCGA-50-5942",
"TCGA-50-6597",
"TCGA-55-1592",
"TCGA-55-1595",
"TCGA-55-6969",
"TCGA-55-6972",
"TCGA-55-6982",
"TCGA-55-7281",
"TCGA-55-7570",
"TCGA-55-7911",
"TCGA-55-8085",
"TCGA-55-8090",
"TCGA-55-8207",
"TCGA-55-8614",
"TCGA-55-8615",
"TCGA-62-A46P",
"TCGA-64-1676",
"TCGA-64-5774",
"TCGA-67-4679",
"TCGA-67-6217",
"TCGA-69-8254",
"TCGA-73-4662",
"TCGA-73-4668",
"TCGA-73-4677",
"TCGA-75-5146",
"TCGA-75-6206",
"TCGA-78-7162",
"TCGA-78-7166",
"TCGA-78-7167",
"TCGA-78-7220",
"TCGA-86-7701",
"TCGA-86-7711",
"TCGA-86-8074",
"TCGA-86-8280",
"TCGA-86-8674",
"TCGA-91-6835",
"TCGA-91-6840",
"TCGA-93-7347",
"TCGA-93-A4JN",
"TCGA-93-A4JP",
"TCGA-99-8025",
"TCGA-J2-A4AG",
"TCGA-L9-A50W",
"TCGA-MP-A4T7",
"TCGA-MP-A4TE",
"TCGA-MP-A5C7",
"TCGA-NJ-A4YP",
"TCGA-05-4244",
"TCGA-05-4384",
"TCGA-05-4403",
"TCGA-05-5425",
"TCGA-35-4123",
"TCGA-44-6774",
"TCGA-44-7670",
"TCGA-44-8117",
"TCGA-49-4512",
"TCGA-50-5055",
"TCGA-50-6594",
"TCGA-53-7813",
"TCGA-55-6968",
"TCGA-55-6980",
"TCGA-55-8092",
"TCGA-55-8206",
"TCGA-55-A48Z",
"TCGA-62-8394",
"TCGA-62-8397",
"TCGA-62-A46U",
"TCGA-62-A46V",
"TCGA-64-5779",
"TCGA-73-7498",
"TCGA-75-7025",
"TCGA-78-7633",
"TCGA-78-8662",
"TCGA-83-5908",
"TCGA-86-8056",
"TCGA-86-8673",
"TCGA-86-A4P7",
"TCGA-91-7771",
"TCGA-93-7348",
"TCGA-93-A4JQ",
"TCGA-95-8039",
"TCGA-95-8494",
"TCGA-95-A4VN",
"TCGA-97-7937",
"TCGA-97-7941",
"TCGA-97-8171",
"TCGA-97-8174",
"TCGA-97-8175",
"TCGA-97-8547",
"TCGA-97-A4M0",
"TCGA-97-A4M1",
"TCGA-97-A4M3",
"TCGA-J2-8192",
"TCGA-J2-8194",
"TCGA-L9-A444",
"TCGA-L9-A7SV",
"TCGA-MP-A4T2",
"TCGA-MP-A4T6",
"TCGA-MP-A4T8",
"TCGA-MP-A4TK",
"TCGA-NJ-A55O",
"TCGA-05-4396",
"TCGA-05-4417",
"TCGA-05-4425",
"TCGA-05-5423",
"TCGA-35-3615",
"TCGA-44-2656",
"TCGA-44-2657",
"TCGA-44-2666",
"TCGA-44-5644",
"TCGA-44-6778",
"TCGA-44-7660",
"TCGA-44-8120",
"TCGA-49-4501",
"TCGA-49-4506",
"TCGA-49-6743",
"TCGA-49-AARO",
"TCGA-50-5049",
"TCGA-50-5072",
"TCGA-50-5931",
"TCGA-50-5933",
"TCGA-50-6595",
"TCGA-50-7109",
"TCGA-50-8460",
"TCGA-53-7626",
"TCGA-53-A4EZ",
"TCGA-55-6712",
"TCGA-55-6975",
"TCGA-55-7724",
"TCGA-55-7726",
"TCGA-55-7727",
"TCGA-55-7728",
"TCGA-55-7815",
"TCGA-62-8398",
"TCGA-62-A46R",
"TCGA-62-A471",
"TCGA-64-1679",
"TCGA-67-3771",
"TCGA-69-7763",
"TCGA-73-4675",
"TCGA-75-5126",
"TCGA-75-7031",
"TCGA-78-7147",
"TCGA-78-7155",
"TCGA-78-7160",
"TCGA-78-7163",
"TCGA-78-7539",
"TCGA-86-7713",
"TCGA-86-8054",
"TCGA-86-8075",
"TCGA-86-8671",
"TCGA-86-8672",
"TCGA-91-6848",
"TCGA-93-8067",
"TCGA-97-7547",
"TCGA-97-7552",
"TCGA-97-7938",
"TCGA-97-8176",
"TCGA-97-8179",
"TCGA-L4-A4E5",
"TCGA-L9-A443",
"TCGA-MN-A4N5",
"TCGA-MP-A4SV",
"TCGA-MP-A4SW",
"TCGA-MP-A4TD",
"TCGA-NJ-A4YI",
"TCGA-S2-AA1A",
"TCGA-05-4390",
"TCGA-05-4430",
"TCGA-35-5375",
"TCGA-38-4627",
"TCGA-44-3398",
"TCGA-44-6144",
"TCGA-44-6777",
"TCGA-44-6779",
"TCGA-44-7667",
"TCGA-44-A47F",
"TCGA-49-4487",
"TCGA-49-4494",
"TCGA-49-6744",
"TCGA-49-6761",
"TCGA-49-AAR9",
"TCGA-49-AARE",
"TCGA-4B-A93V",
"TCGA-50-5044",
"TCGA-50-5066",
"TCGA-50-6590",
"TCGA-55-6981",
"TCGA-55-6986",
"TCGA-55-7284",
"TCGA-55-7573",
"TCGA-55-7725",
"TCGA-55-7914",
"TCGA-55-8087",
"TCGA-55-8091",
"TCGA-55-8096",
"TCGA-55-8097",
"TCGA-55-8205",
"TCGA-55-8301",
"TCGA-55-8508",
"TCGA-55-8514",
"TCGA-55-8619",
"TCGA-55-A494",
"TCGA-55-A57B",
"TCGA-62-8399",
"TCGA-62-A46Y",
"TCGA-62-A470",
"TCGA-69-7761",
"TCGA-69-7765",
"TCGA-73-7499",
"TCGA-75-5122",
"TCGA-75-5147",
"TCGA-75-6214",
"TCGA-75-7027",
"TCGA-78-7146",
"TCGA-78-7149",
"TCGA-78-8655",
"TCGA-80-5607",
"TCGA-86-8073",
"TCGA-86-8278",
"TCGA-86-8668",
"TCGA-86-A4P8",
"TCGA-91-6831",
"TCGA-91-8496",
"TCGA-97-7546",
"TCGA-99-AA5R",
"TCGA-L9-A5IP",
"TCGA-NJ-A55A",
"TCGA-NJ-A7XG",
"TCGA-05-4395",
"TCGA-05-4397",
"TCGA-44-2662",
"TCGA-44-6776",
"TCGA-44-7659",
"TCGA-44-7672",
"TCGA-44-8119",
"TCGA-44-A47A",
"TCGA-44-A4SS",
"TCGA-49-4507",
"TCGA-49-4514",
"TCGA-49-AAR0",
"TCGA-49-AAR2",
"TCGA-50-5045",
"TCGA-50-5939",
"TCGA-55-1594",
"TCGA-55-6971",
"TCGA-55-6978",
"TCGA-55-6979",
"TCGA-55-7283",
"TCGA-55-7910",
"TCGA-55-7995",
"TCGA-55-8089",
"TCGA-55-8208",
"TCGA-55-8302",
"TCGA-55-8505",
"TCGA-55-8616",
"TCGA-55-A490",
"TCGA-62-8395",
"TCGA-62-A46S",
"TCGA-64-5778",
"TCGA-67-6215",
"TCGA-67-6216",
"TCGA-69-7764",
"TCGA-69-A59K",
"TCGA-73-4666",
"TCGA-75-6205",
"TCGA-78-7148",
"TCGA-78-7153",
"TCGA-78-7156",
"TCGA-78-7161",
"TCGA-78-8640",
"TCGA-80-5608",
"TCGA-86-6851",
"TCGA-86-8358",
"TCGA-86-8359",
"TCGA-86-A4JF",
"TCGA-91-6830",
"TCGA-91-6847",
"TCGA-95-7039",
"TCGA-95-7562",
"TCGA-95-7567",
"TCGA-97-7553",
"TCGA-97-A4M6",
"TCGA-99-7458",
"TCGA-J2-A4AD",
"TCGA-L9-A8F4",
"TCGA-MP-A4T4",
"TCGA-MP-A4TH",
"TCGA-NJ-A4YG",
"TCGA-O1-A52J",
"TCGA-05-4382",
"TCGA-05-4432",
"TCGA-05-4434",
"TCGA-05-5715",
"TCGA-44-2655",
"TCGA-44-3396",
"TCGA-44-3919",
"TCGA-44-A4SU",
"TCGA-49-4486",
"TCGA-49-4505",
"TCGA-49-6745",
"TCGA-49-AAR4",
"TCGA-50-5051",
"TCGA-50-5936",
"TCGA-50-5941",
"TCGA-50-6593",
"TCGA-50-6673",
"TCGA-55-5899",
"TCGA-55-6543",
"TCGA-55-6642",
"TCGA-55-6970",
"TCGA-55-6987",
"TCGA-55-7574",
"TCGA-55-7576",
"TCGA-55-7994",
"TCGA-55-8203",
"TCGA-55-8204",
"TCGA-55-8510",
"TCGA-55-8512",
"TCGA-55-8620",
"TCGA-55-A491",
"TCGA-55-A492",
"TCGA-55-A493",
"TCGA-55-A4DF",
"TCGA-55-A4DG",
"TCGA-62-8402",
"TCGA-62-A46O",
"TCGA-64-5815",
"TCGA-67-3774",
"TCGA-71-6725",
"TCGA-71-8520",
"TCGA-73-4676",
"TCGA-75-6207",
"TCGA-75-6212",
"TCGA-78-7145",
"TCGA-78-7536",
"TCGA-78-7540",
"TCGA-91-8497",
"TCGA-95-7944",
"TCGA-95-7947",
"TCGA-95-7948",
"TCGA-97-8177",
"TCGA-97-A4LX",
"TCGA-97-A4M2",
"TCGA-97-A4M7",
"TCGA-99-8028",
"TCGA-MP-A4SY",
"TCGA-NJ-A55R",
"TCGA-05-4249",
"TCGA-05-4250",
"TCGA-05-4405",
"TCGA-05-4418",
"TCGA-05-4420",
"TCGA-05-4422",
"TCGA-05-4424",
"TCGA-05-4427",
"TCGA-05-5428",
"TCGA-38-4625",
"TCGA-38-7271",
"TCGA-38-A44F",
"TCGA-44-2665",
"TCGA-44-2668",
"TCGA-44-3918",
"TCGA-44-4112",
"TCGA-44-7661",
"TCGA-44-7669",
"TCGA-44-A47G",
"TCGA-49-4490",
"TCGA-49-AAR3",
"TCGA-50-5935",
"TCGA-50-5944",
"TCGA-50-6591",
"TCGA-50-6592",
"TCGA-50-8457",
"TCGA-53-7624",
"TCGA-55-1596",
"TCGA-55-6985",
"TCGA-55-7227",
"TCGA-55-7913",
"TCGA-55-8506",
"TCGA-55-8507",
"TCGA-55-8621",
"TCGA-55-A48X",
"TCGA-64-1680",
"TCGA-64-5775",
"TCGA-64-5781",
"TCGA-67-3773",
"TCGA-69-7973",
"TCGA-69-7978",
"TCGA-69-8253",
"TCGA-69-8255",
"TCGA-73-4659",
"TCGA-73-4670",
"TCGA-73-A9RS",
"TCGA-75-6203",
"TCGA-75-6211",
"TCGA-78-7152",
"TCGA-78-7535",
"TCGA-78-8660",
"TCGA-86-6562",
"TCGA-86-7714",
"TCGA-86-7954",
"TCGA-86-8055",
"TCGA-86-8076",
"TCGA-86-8279",
"TCGA-86-8281",
"TCGA-86-8585",
"TCGA-86-8669",
"TCGA-86-A456",
"TCGA-91-6849",
"TCGA-91-8499",
"TCGA-93-A4JO",
"TCGA-95-7043",
"TCGA-95-A4VP",
"TCGA-97-8172",
"TCGA-97-8552",
"TCGA-97-A4M5",
"TCGA-99-8032",
"TCGA-99-8033",
"TCGA-J2-A4AE",
"TCGA-L4-A4E6",
"TCGA-L9-A743",
"TCGA-MN-A4N1",
"TCGA-MN-A4N4",
"TCGA-MP-A4TF",
"TCGA-NJ-A4YQ"),
legacy = TRUE)
GDCdownload(query, method = "api", files.per.chunk = 10)
data3 <- GDCprepare(query)
write.csv(data3@assays@data, file="LUAD-Assays.csv", row.names = TRUE)