Load TARGET huex data as SummarizedExperiment
target_huex_se()
res = target_huex_se()#> #> #> #>#>#> #> #> #> col_date(format = ""), #> col_logical(), #> col_double(), #> col_double(), #> col_double(), #> col_double() #>#>res#> class: SummarizedExperiment #> dim: 22011 89 #> metadata(0): #> assays(1): exprs #> rownames(22011): 3948543 3063807 ... 2968418 3275568 #> rowData names(3): symbol tx_list symbol_list #> colnames(89): PATKSS PAUTWB ... 0A4HMC PASUUH #> colData names(33): TARGET USI Gender ... Percent necrosis at Definitive #> Surgery metastatic#> DataFrame with 6 rows and 33 columns #> TARGET USI Gender Race Ethnicity #> <character> <character> <character> <character> #> PATKSS PATKSS Male White Not Hispanic or Latino #> PAUTWB PAUTWB Male White Not Hispanic or Latino #> PAUTYB PAUTYB Female White Hispanic or Latino #> PAUUML PAUUML Male Unknown Hispanic or Latino #> PAUVUL PAUVUL Female Black or African American Not Hispanic or Latino #> PAUXPZ PAUXPZ Female Unknown Unknown #> Age at Diagnosis in Days First Event Time to First Event in Days #> <numeric> <character> <numeric> #> PATKSS 4889 Relapse 63 #> PAUTWB 5064 Relapse 598 #> PAUTYB 4418 Relapse 527 #> PAUUML 2177 No event 672 #> PAUVUL 2027 Relapse 237 #> PAUXPZ 4507 Relapse 419 #> Vital Status Overall Survival Time in Days Year of Diagnosis #> <character> <numeric> <numeric> #> PATKSS Dead 758 2010 #> PAUTWB Alive 687 2012 #> PAUTYB Dead 537 2012 #> PAUUML Alive 672 2012 #> PAUVUL Dead 347 2012 #> PAUXPZ Dead 606 2012 #> Year of Last Follow Up Protocol Disease at diagnosis #> <numeric> <character> <character> #> PATKSS 2012 AOST0331 Non-metastatic (confirmed) #> PAUTWB 2014 AOST06B1 Non-metastatic (confirmed) #> PAUTYB 2013 AOST06B1 Non-metastatic (confirmed) #> PAUUML 2014 AOST06B1 Non-metastatic (confirmed) #> PAUVUL 2013 AOST06B1 Metastatic (confirmed) #> PAUXPZ 2014 AOST06B1 Metastatic (confirmed) #> Metastasis site Primary tumor site Specific tumor site #> <character> <character> <character> #> PATKSS NA Pelvis Pelvis / Sacrum #> PAUTWB NA Leg/foot Tibia #> PAUTYB NA Leg/foot Tibia #> PAUUML NA Leg/foot Femur #> PAUVUL Lung only Leg/foot Femur #> PAUXPZ Lung only Leg/foot Tibia #> Specific tumor side Specific tumor region Definitive Surgery #> <character> <character> <character> #> PATKSS NA NA Limb sparing #> PAUTWB NA NA NA #> PAUTYB NA NA NA #> PAUUML NA NA NA #> PAUVUL NA NA NA #> PAUXPZ NA NA NA #> Primary site progression Site of initial relapse #> <character> <character> #> PATKSS Yes NA #> PAUTWB NA NA #> PAUTYB NA NA #> PAUUML NA NA #> PAUVUL NA NA #> PAUXPZ NA NA #> Time to first relapse in days #> <numeric> #> PATKSS 63 #> PAUTWB 598 #> PAUTYB 527 #> PAUUML NA #> PAUVUL 237 #> PAUXPZ 419 #> Time to first enrollment on relapse protocol in days #> <numeric> #> PATKSS NA #> PAUTWB NA #> PAUTYB NA #> PAUUML NA #> PAUVUL NA #> PAUXPZ NA #> Time to first SMN in days Time to death in days Histologic response #> <numeric> <numeric> <character> #> PATKSS NA 758 0-90 #> PAUTWB NA NA NA #> PAUTYB NA 537 NA #> PAUUML NA NA NA #> PAUVUL NA 347 NA #> PAUXPZ NA 724 NA #> Percent necrosis Relapse Type Therapy Comment cohort #> <character> <character> <character> <character> <character> #> PATKSS NA NA NA NA Discovery #> PAUTWB NA NA NA NA Discovery #> PAUTYB NA NA NA NA Discovery #> PAUUML NA NA NA NA Discovery #> PAUVUL NA NA NA NA Discovery #> PAUXPZ NA NA NA NA Discovery #> Percent necrosis at Definitive Surgery metastatic #> <character> <logical> #> PATKSS NA FALSE #> PAUTWB NA FALSE #> PAUTYB NA FALSE #> PAUUML NA FALSE #> PAUVUL NA TRUE #> PAUXPZ NA TRUEassay(res,'exprs')[1:5,1:5]#> PATKSS PAUTWB PAUTYB PAUUML PAUVUL #> 3948543 8.28067 8.39749 8.23240 9.34217 7.71883 #> 3063807 8.24085 8.42118 8.06178 8.04157 8.01377 #> 3096575 10.53751 9.82508 9.80597 9.32693 9.23512 #> 2949118 7.39632 7.84181 7.37891 7.28287 7.70401 #> 3227645 10.20303 9.83912 9.80234 10.56681 9.08011#> DataFrame with 6 rows and 3 columns #> symbol tx_list #> <character> <List> #> 3948543 FAM118A ENST00000216214,NM_001104595,NM_017911,... #> 3063807 GPC2 ENST00000471717,ENST00000480087,ENST00000490629,... #> 3096575 HGSNAT NM_152419,ENST00000458501,ENST00000379644,... #> 2949118 LTB ENST00000457552,ENST00000456113,ENST00000446745,... #> 3227645 UCK1 NM_001261451,NM_031432,ENST00000372215,... #> 4014076 HDX NM_001177479,NM_144657,NM_001177478,... #> symbol_list #> <List> #> 3948543 FAM118A #> 3063807 GPC2 #> 3096575 HGSNAT,METTL21A,LOC100653153,... #> 2949118 LTB #> 3227645 UCK1 #> 4014076 HDX