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) {
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)
                 )
)
}