pathologicM=clinical$ajcc_pathologic_m pathologicN=clinical$ajcc_pathologic_n #提取stage分期 pathologicStage=clinical$ajcc_pathologic_stage 3)合并临床信息 #合并信息 TCGA_merge=cbind(ID, age, gender, time, status, pathologicT, pathologicM, pathologicN, pathologicStage) 4)删除缺失值并导出 #删除缺失...
"submitter_id", "days_to_last_follow_up", "vital_status", "ajcc_pathologic_t", "ajcc_pathologic_n", "ajcc_pathologic_m", "ajcc_pathologic_stage", "gender" )) %>% `names<-`(c("Tumor_Sample_Barcode", "time", "status", "T", "N", "M", "stage", "gender")) paad.maf <-...
clin1 <-clin %>% select(sample,'cancer type abbreviation',gender,ajcc_pathologic_tumor_stage,OS,OS.time) %>% #选取这些列 rename(Type='cancer type abbreviation',Stage=ajcc_pathologic_tumor_stage,status=OS,time=OS.time)读取基因注释文件（详见TCGA数据下载与ID转换）gtf <- rtracklayer::impo...
## [13] "ajcc_pathologic_stage" "days_to_diagnosis" ## [15] "treatments" "last_known_disease_status"## [17] "tissue_or_organ_of_origin" "days_to_last_follow_up" ## [19] "age_at_diagnosis" "primary_diagnosis" ## [21] "prior_malignancy" 现在一共有698行,107列临床信息,你想要...
[3]"synchronous_malignancy""ajcc_pathologic_stage" [5]"days_to_diagnosis""last_known_disease_status" [7]"tissue_or_organ_of_origin""days_to_last_follow_up" [9]"age_at_diagnosis""primary_diagnosis" [11]"prior_malignancy""year_of_diagnosis" ...
'AJCC_PATHOLOGIC_TUMOR_STAGE','AJCC_TUMOR_PATHOLOGIC_PT',"AGE",'SEX','VITAL_STATUS','OS_STATUS','OS_MONTHS',"DFS_MONTHS","DFS_STATUS")choose_clinicaldata=myclinicaldata[,choose_columns]colnames(choose_clinicaldata)[1:4]=c('M','N','STAGE','T')str(choose_clinicaldata,no.list=T,...
("case_id","Tumor_Sample_Barcode","vital_status","days_to_last_follow_up","ajcc_pathologic_m","ajcc_pathologic_n","ajcc_pathologic_stage","ajcc_pathologic_t")clin1<-clin1[clin1$days_to_last_follow_up!="--",]clin1$days_to_last_follow_up<-as.numeric(clin1$days_to_last_follow_...
[11] "tissue_type" "synchronous_malignancy" ## [13] "ajcc_pathologic_stage" "days_to_diagnosis" ## [15] "treatments" "last_known_disease_status" ## [17] "tissue_or_organ_of_origin" "days_to_last_follow_up" ## [19] "age_at_diagnosis" "primary_diagnosis" ## [21] "prior_...
## [13] "ajcc_pathologic_stage" "days_to_diagnosis" ## [15] "treatments" "last_known_disease_status" ## [17] "tissue_or_organ_of_origin" "days_to_last_follow_up" ## [19] "age_at_diagnosis" "primary_diagnosis" ## [21] "prior_malignancy" ...
LIHCData<-group_by(data,AGE,SEX,AJCC_PATHOLOGIC_TUMOR_STAGE,OS_STATUS)%>%summarise(.,count=n()) #查看宽数据格式 head(LIHCData) AGESEXAJCC_PATHOLOGIC_TUMOR_STAGEOS_STATUScount <fct><fct><fct><fct><int> 150to70FemaleSTAGEIDECEASED11 ...