My goal is to produce an OncoPlot with somatic mutation, copy number, and clinical information.

I'm able to produce a MAF file with clinical info:

maf.plus.clin <- read.maf(
  maf = maf,
  clinicalData = clinical.all,
)

and also a MAF file with GISTIC info:

maf.plus.gistic <- read.maf(
  maf = maf,
  gisticAllLesionsFile = all.lesions,
  gisticAmpGenesFile = amp.genes,
  gisticDelGenesFile = del.genes,
  gisticScoresFile = scores.gis,
  isTCGA = TRUE,
  verbose = FALSE, 
)

However, clinical info is absent when I combine

maf.plus.gistic.plus.clin <- read.maf(
  maf = maf,
  gisticAllLesionsFile = all.lesions,
  gisticAmpGenesFile = amp.genes,
  gisticDelGenesFile = del.genes,
  gisticScoresFile = scores.gis,
  isTCGA = TRUE,
  verbose = FALSE, 
  clinicalData = clinical.all,
)

Output:

> dput(maf.plus.clin@clinical.data[1:5,1:5])
structure(list(project = c("TCGA-KIRP", "TCGA-KIRP", "TCGA-KIRP", 
"TCGA-KIRP", "TCGA-KIRP"), submitter_id = c("TCGA-2K-A9WE", "TCGA-2Z-A9J1", 
"TCGA-2Z-A9J2", "TCGA-2Z-A9J3", "TCGA-2Z-A9J5"), synchronous_malignancy = c("No", 
"No", "No", "No", "No"), ajcc_pathologic_stage = c("Stage II", 
"Stage I", "Stage I", "Stage II", "Stage II"), days_to_diagnosis = c("0", 
"0", "0", "0", "0")), class = c("data.table", "data.frame"), row.names = c(NA, 
-5L), .internal.selfref = <pointer: 0x2ac52cc4f2b0>)

> dput(maf.plus.gistic@clinical.data[1:5,])
structure(list(Tumor_Sample_Barcode = c("TCGA-2K-A9WE", "TCGA-2Z-A9J1", 
"TCGA-2Z-A9J2", "TCGA-2Z-A9J3", "TCGA-2Z-A9J5")), class = c("data.table", 
"data.frame"), row.names = c(NA, -5L), .internal.selfref = <pointer: 0x2ac52cc4f2b0>)

> dput(maf.plus.gistic.plus.clin@clinical.data[1:5,1:5])
structure(list(project = c(NA_character_, NA_character_, NA_character_, 
NA_character_, NA_character_), submitter_id = c(NA_character_, 
NA_character_, NA_character_, NA_character_, NA_character_), 
    synchronous_malignancy = c(NA_character_, NA_character_, 
    NA_character_, NA_character_, NA_character_), ajcc_pathologic_stage = c(NA_character_, 
    NA_character_, NA_character_, NA_character_, NA_character_
    ), days_to_diagnosis = c(NA_character_, NA_character_, NA_character_, 
    NA_character_, NA_character_)), class = c("data.table", "data.frame"
), row.names = c(NA, -5L), .internal.selfref = <pointer: 0x2ac52cc4f2b0>)