UCSCXenaShiny (version 2.2.0)

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

Description

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
)

Value

a list object with grouping samples and statistics

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

Examples

if (FALSE) {
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)
  )
)
}