【原】TCGAbiolinks獲取癌癥臨床信息

生信交流平臺(tái) 2021-12-29

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上次我們簡(jiǎn)單的介紹了一下腫瘤的TNM分期系統(tǒng)。今天我們來(lái)用R獲取感興趣的癌癥的臨床信息，其中就可以找到我們上次講到的TNM分期信息,。

#加載TCGAbiolinks包library(TCGAbiolinks)#下載TCGA-CHOL這個(gè)項(xiàng)目相關(guān)的臨床信息,，這個(gè)項(xiàng)目是膽管癌clinical <- GDCquery_clinic(project = "TCGA-CHOL", type = "clinical")#將下載到的臨床信息寫入到clinical.csv文件中write.csv(file="clinical.csv",clinical)

> dim(clinical)[1] 51 158

一共得到51個(gè)樣本的臨床信息,，一共有158條臨床信息,，他們分別是

> names(clinical) [1] "submitter_id" [2] "year_of_diagnosis" [3] "classification_of_tumor" [4] "last_known_disease_status" [5] "updated_datetime" [6] "primary_diagnosis" [7] "tumor_stage" [8] "age_at_diagnosis" [9] "morphology" [10] "days_to_last_known_disease_status" [11] "created_datetime" [12] "prior_treatment" [13] "ajcc_pathologic_n" [14] "ajcc_pathologic_m" [15] "state" [16] "days_to_last_follow_up" [17] "days_to_recurrence" [18] "diagnosis_id" [19] "tumor_grade" [20] "icd_10_code" [21] "days_to_diagnosis" [22] "tissue_or_organ_of_origin" [23] "progression_or_recurrence" [24] "prior_malignancy" [25] "ajcc_staging_system_edition" [26] "ajcc_pathologic_stage" [27] "synchronous_malignancy" [28] "site_of_resection_or_biopsy" [29] "ajcc_pathologic_t" [30] "vascular_invasion_type" [31] "method_of_diagnosis" [32] "laterality" [33] "ann_arbor_pathologic_stage" [34] "inrg_stage" [35] "metastasis_at_diagnosis" [36] "cog_rhabdomyosarcoma_risk_group" [37] "irs_group" [38] "weiss_assessment_score" [39] "enneking_msts_metastasis" [40] "esophageal_columnar_dysplasia_degree" [41] "lymph_nodes_tested" [42] "ishak_fibrosis_score" [43] "lymphatic_invasion_present" [44] "supratentorial_localization" [45] "igcccg_stage" [46] "gastric_esophageal_junction_involvement" [47] "goblet_cells_columnar_mucosa_present" [48] "iss_stage" [49] "enneking_msts_tumor_site" [50] "tumor_regression_grade" [51] "gross_tumor_weight" [52] "ajcc_clinical_stage" [53] "ann_arbor_b_symptoms" [54] "cog_neuroblastoma_risk_group" [55] "days_to_best_overall_response" [56] "enneking_msts_grade" [57] "tumor_largest_dimension_diameter" [58] "figo_stage" [59] "child_pugh_classification" [60] "peripancreatic_lymph_nodes_positive" [61] "circumferential_resection_margin" [62] "lymph_nodes_positive" [63] "inss_stage" [64] "inpc_histologic_group" [65] "secondary_gleason_grade" [66] "residual_disease" [67] "anaplasia_present" [68] "ann_arbor_clinical_stage" [69] "tumor_confined_to_organ_of_origin" [70] "perineural_invasion_present" [71] "tumor_focality" [72] "wilms_tumor_histologic_subtype" [73] "ajcc_clinical_t" [74] "ajcc_clinical_n" [75] "ajcc_clinical_m" [76] "irs_stage" [77] "first_symptom_prior_to_diagnosis" [78] "cog_liver_stage" [79] "enneking_msts_stage" [80] "inpc_grade" [81] "burkitt_lymphoma_clinical_variant" [82] "ann_arbor_extranodal_involvement" [83] "peripancreatic_lymph_nodes_tested" [84] "masaoka_stage" [85] "mitosis_karyorrhexis_index" [86] "esophageal_columnar_metaplasia_present" [87] "best_overall_response" [88] "vascular_invasion_present" [89] "micropapillary_features" [90] "primary_gleason_grade" [91] "anaplasia_present_type" [92] "medulloblastoma_molecular_classification" [93] "cog_renal_stage" [94] "metastasis_at_diagnosis_site" [95] "gleason_grade_group" [96] "NA." [97] "cigarettes_per_day" [98] "weight" [99] "alcohol_history" [100] "alcohol_intensity" [101] "bmi" [102] "years_smoked" [103] "exposure_id" [104] "height" [105] "environmental_tobacco_smoke_exposure" [106] "tobacco_smoking_status" [107] "pack_years_smoked" [108] "respirable_crystalline_silica_exposure" [109] "coal_dust_exposure" [110] "asbestos_exposure" [111] "type_of_tobacco_used" [112] "tobacco_smoking_onset_year" [113] "smoking_frequency" [114] "tobacco_smoking_quit_year" [115] "type_of_smoke_exposure" [116] "alcohol_days_per_week" [117] "time_between_waking_and_first_smoke" [118] "radon_exposure" [119] "alcohol_drinks_per_day" [120] "gender" [121] "year_of_birth" [122] "race" [123] "days_to_birth" [124] "ethnicity" [125] "vital_status" [126] "demographic_id" [127] "age_at_index" [128] "year_of_death" [129] "days_to_death" [130] "cause_of_death" [131] "weeks_gestation_at_birth" [132] "premature_at_birth" [133] "treatments_pharmaceutical_days_to_treatment_start" [134] "treatments_pharmaceutical_treatment_effect" [135] "treatments_pharmaceutical_initial_disease_status" [136] "treatments_pharmaceutical_treatment_type" [137] "treatments_pharmaceutical_treatment_id" [138] "treatments_pharmaceutical_therapeutic_agents" [139] "treatments_pharmaceutical_regimen_or_line_of_therapy"[140] "treatments_pharmaceutical_treatment_intent_type" [141] "treatments_pharmaceutical_treatment_anatomic_site" [142] "treatments_pharmaceutical_treatment_outcome" [143] "treatments_pharmaceutical_days_to_treatment_end" [144] "treatments_pharmaceutical_treatment_or_therapy" [145] "treatments_radiation_days_to_treatment_start" [146] "treatments_radiation_treatment_effect" [147] "treatments_radiation_initial_disease_status" [148] "treatments_radiation_treatment_type" [149] "treatments_radiation_treatment_id" [150] "treatments_radiation_therapeutic_agents" [151] "treatments_radiation_regimen_or_line_of_therapy" [152] "treatments_radiation_treatment_intent_type" [153] "treatments_radiation_treatment_anatomic_site" [154] "treatments_radiation_treatment_outcome" [155] "treatments_radiation_days_to_treatment_end" [156] "treatments_radiation_treatment_or_therapy" [157] "bcr_patient_barcode" [158] "disease"

我們上次提到的TNM分期信息在這里的名字分別叫"ajcc_pathologic_t","ajcc_pathologic_n"和"ajcc_pathologic_m" ,。

這個(gè)文件也保存到本地了,，我們可以直接用Excel打開查看,，并找到這三列。