Group TPC samples by build-in or custom phenotype and support filtering or merging operations

Usage

query_tcga_group(
  database = c("toil", "pcawg", "ccle"),
  cancer = NULL,
  custom = NULL,
  group = "Gender",
  filter_by = NULL,
  filter_id = NULL,
  merge_by = NULL,
  merge_quantile = FALSE,
  return_all = FALSE
)

Arguments

database: one of c("toil","pcawg","ccle")
cancer: select cancer cohort(s)
custom: upload custom phenotype data
group: target group names
filter_by: filter samples by one or multiple criterion
filter_id: directly filter samples by provided sample ids
merge_by: merge the target group for main categories
merge_quantile: whether to merge numerical variable by percentiles
return_all: return the all phenotype data

Value

a list object with grouping samples and statistics

Examples

if (FALSE) { # \dontrun{
query_tcga_group(group = "Age")

query_tcga_group(
  cancer = "BRCA",
  group = "Stage_ajcc"
)

query_tcga_group(
  cancer = "BRCA",
  group = "Stage_ajcc",
  filter_by = list(
    c("Code", c("TP"), "+"),
    c("Stage_ajcc", c(NA), "-")
  )
)

query_tcga_group(
  cancer = "BRCA",
  group = "Stage_ajcc",
  filter_by = list(
    c("Age", c(0.5), "%>")
  )
)

query_tcga_group(
  cancer = "BRCA",
  group = "Stage_ajcc",
  filter_by = list(
    c("Age", c(60), ">")
  )
)

query_tcga_group(
  cancer = "BRCA",
  group = "Stage_ajcc",
  merge_by = list(
    "Early" = c("Stage I"),
    "Late" = c("Stage II", "Stage III", "Stage IV")
  )
)

query_tcga_group(
  cancer = "BRCA",
  group = "Age",
  merge_by = list(
    "Young" = c(20, 60),
    "Old" = c(60, NA)
  )
)

query_tcga_group(
  cancer = "BRCA",
  group = "Age",
  merge_quantile = TRUE,
  merge_by = list(
    "Young" = c(0, 0.5),
    "Old" = c(0.5, 1)
  )
)
} # }