load TARGET GISTIC data as summarized experiment
target_gistic_se()
res = target_gistic_se()#> #> #> #>#>res#> class: SummarizedExperiment #> dim: 23109 88 #> metadata(0): #> assays(1): cn #> rownames: NULL #> rowData names(3): Gene Symbol Locus ID Cytoband #> colnames(88): 0A4HLD 0A4HMC ... PAPWWC PATEEM #> colData names(33): TARGET USI Gender ... Percent necrosis at Definitive #> Surgery metastatic#> DataFrame with 6 rows and 33 columns #> TARGET USI Gender Race Ethnicity Age at Diagnosis in Days #> <character> <character> <character> <character> <numeric> #> 0A4HLD 0A4HLD Male NA NA 7254 #> 0A4HMC 0A4HMC Male White NA 10205 #> 0A4HX8 0A4HX8 Male White NA 10635 #> 0A4HXS 0A4HXS Male White NA 8470 #> 0A4HY5 0A4HY5 Male NA NA 7264 #> 0A4I0Q 0A4I0Q Female NA NA 7269 #> First Event Time to First Event in Days Vital Status #> <character> <numeric> <character> #> 0A4HLD Censored 3946 Alive #> 0A4HMC Censored 377 Alive #> 0A4HX8 Censored 3050 Alive #> 0A4HXS Censored 2948 Alive #> 0A4HY5 Relapse 218 Dead #> 0A4I0Q Death 519 Dead #> Overall Survival Time in Days Year of Diagnosis Year of Last Follow Up #> <numeric> <numeric> <numeric> #> 0A4HLD 3946 2000 2011 #> 0A4HMC 377 NA NA #> 0A4HX8 1750 2003 2011 #> 0A4HXS 2948 2004 2014 #> 0A4HY5 290 2004 2005 #> 0A4I0Q 519 2005 2006 #> Protocol Disease at diagnosis Metastasis site #> <character> <character> <character> #> 0A4HLD IHRT Non-metastatic (confirmed) NA #> 0A4HMC IHRT Non-metastatic (confirmed) NA #> 0A4HX8 IHRT Non-metastatic (confirmed) NA #> 0A4HXS IHRT Non-metastatic (confirmed) NA #> 0A4HY5 IHRT Metastatic Lung only #> 0A4I0Q IHRT Metastatic Lung only #> Primary tumor site Specific tumor site Specific tumor side #> <character> <character> <character> #> 0A4HLD Leg/Foot Tibia NA #> 0A4HMC Leg/Foot Fibula NA #> 0A4HX8 Leg/Foot Femur NA #> 0A4HXS Leg/Foot Femur NA #> 0A4HY5 Leg/Foot Pelvis NA #> 0A4I0Q Leg/Foot Femur NA #> Specific tumor region Definitive Surgery Primary site progression #> <character> <character> <character> #> 0A4HLD Proximal Limb sparing No #> 0A4HMC Other, Not specified Amputation No #> 0A4HX8 Distal Limb sparing No #> 0A4HXS Distal Limb sparing No #> 0A4HY5 Other, Posterior Limb sparing No #> 0A4I0Q Distal Limb sparing No #> Site of initial relapse Time to first relapse in days #> <character> <numeric> #> 0A4HLD NA NA #> 0A4HMC NA NA #> 0A4HX8 NA NA #> 0A4HXS NA NA #> 0A4HY5 Regional Lymph nodes 218 #> 0A4I0Q NA NA #> Time to first enrollment on relapse protocol in days #> <numeric> #> 0A4HLD NA #> 0A4HMC NA #> 0A4HX8 NA #> 0A4HXS NA #> 0A4HY5 NA #> 0A4I0Q NA #> Time to first SMN in days Time to death in days Histologic response #> <numeric> <numeric> <character> #> 0A4HLD NA NA Stage 3/4 #> 0A4HMC NA NA Stage 1/2 #> 0A4HX8 NA NA Stage 3/4 #> 0A4HXS NA NA Stage 1/2 #> 0A4HY5 NA 290 Stage 1/2 #> 0A4I0Q NA 519 Stage 1/2 #> Percent necrosis Relapse Type #> <character> <character> #> 0A4HLD 99 NA #> 0A4HMC 60 NA #> 0A4HX8 100 NA #> 0A4HXS 40 NA #> 0A4HY5 50 NA #> 0A4I0Q < 50 NA #> Therapy #> <character> #> 0A4HLD MTX/Adria/Ifos/±Plat #> 0A4HMC Adria/Plat #> 0A4HX8 Pre-op Adria/Ifos/MTX + Adria/Plat; Post-op Adria/Plat + Adria/Ifos #> 0A4HXS Adria/Plat/MTX #> 0A4HY5 Adria/Plat/MTX #> 0A4I0Q MTX/Adria/Ifos/±Plat #> Comment cohort Percent necrosis at Definitive Surgery #> <character> <character> <character> #> 0A4HLD NA Discovery NA #> 0A4HMC NA Discovery NA #> 0A4HX8 NA Discovery NA #> 0A4HXS NA Discovery NA #> 0A4HY5 NA Discovery NA #> 0A4I0Q NA Discovery NA #> metastatic #> <logical> #> 0A4HLD FALSE #> 0A4HMC FALSE #> 0A4HX8 FALSE #> 0A4HXS FALSE #> 0A4HY5 TRUE #> 0A4I0Q TRUEassay(res,'cn')[1:5,1:5]#> 0A4HLD 0A4HMC 0A4HX8 0A4HXS 0A4HY5 #> [1,] -0.498 0.27 -0.465 0.203 0.11 #> [2,] -0.498 0.27 -0.465 0.203 0.11 #> [3,] -0.498 0.27 -0.465 0.203 0.11 #> [4,] -0.498 0.27 -0.465 0.203 0.11 #> [5,] -0.498 0.27 -0.465 0.203 0.11