这里我们以clinical文件作为展示,可以发现case_id这里有重复的,经过对比,发现重复的case_id只有treatment_type是不一样的,也就是接受的治疗方式有多种,如下图: 好的,现在表达量数据有了,病人的信息也有了。下节我们看如何将表达量信息和病人信息结合在一起。
type="n",axes=F,xlab="",ylab="") text.cex=0.8 text(0,n:1,gene,adj=0,cex=text.cex)...
clinical.indexed <- GDCquery_clinic(project ="TCGA-COAD", type ="clinical") dim(clinical.indexed) ## [1] 461 70 #colnames(clinical.indexed) 一共70列,虽然列名中有一些和化疗药物、放疗有关,但是并没有用药信息(可以自己点开看看)。 这个indexed clinical data是从XML整理出来的,虽然没有XML全,但是...
Clinical information about participants (e.g., sex, race, ethnicity, drugs taken, and response to treatment); Information about the samples (e.g., the weight of a sample portion, days to collect, and time of freezing); and Images of the tumors (allows estimation of number of proliferating...
For these patients, postoperative supplementary treatment is necessary to avoid inadequate treatment. However, there are some studies have shown that targeted therapy is more effective for CN-H type patients. The TCGA molecular typing of EC has overcome the limitations of traditional pathological and ...
antirefux_treatment_types-antirefux_treatment_type barretts_esophagus巴雷特食管(食管下端有不正常的柱状上皮覆盖,并与反流性食管炎密切相关) bcr_patient_barcode bcr_patient_uuid city_o_procurement患者录入信息时的城市 country_o_procurement患者录入信息时的国家 ...
file.type = "results", barcode = listSamples, legacy = TRUE ) # 下载 IlluminaHiSeq_RNASeqV2 平台中对应样本的信息GDCdownload(query) # 处理成行尾 geneID 列为样本 (barcode) 的矩阵 BRCARnaseqSE <-GDCprepare(query) # 获取表达谱 BRCAMatrix <- assay(BRCARnaseqSE,"raw_count") ...
Listage_at_initial_pathologic_diagnosisanatomic_neoplasm_subdivisionanatomic_neoplasm_subdivision_otherantireflux_treatmentantireflux_treatment_types-antireflux_treatment_typebarretts_esophagusbcr_patient_barcodebcr_patient_uuidcity_of_procurementcountry_of_procurement day_of_form_completiondays_to_birthdays_to_...
library(stringr) # 行名ID转换:方法1(推荐) head(rownames(exp)) library(AnnoProbe) annoGene(rownames(exp),ID_type = "ENSEMBL") # 转换不了 rownames(exp) = str_split(rownames(exp),"\\.",simplify = T)[,1];head(rownames(exp)) re = annoGene(rownames(exp),ID_type = "ENSEMBL")...
_freedays_to_recurrencediabetes_treatment_typedisease_responsedlco_ref_predictive_percentecog_performance_statusevidence_of_recurrence_typefev1_fvc_post_bronch_percentfev1_fvc_pre_bronch_percentfev1_ref_post_bronch_percentfev1_ref_pre_bronch_percenthaart_treatment_indicatorheighthepatitis_sustained_virological_...