tcga survival analysis {UCSCXenaShiny}

TCGA Survival Analysis

Description

• Firstly, get merged data of one molecular profile value and associated clinical data from TCGA Pan-Cancer dataset.

• Secondly, filter data as your wish.

• Finally, show K-M plot.

Usage

tcga_surv_get(
  item,
  TCGA_cohort = "LUAD",
  profile = c("mRNA", "miRNA", "methylation", "transcript", "protein", "mutation", "cnv"),
  TCGA_cli_data = dplyr::full_join(load_data("tcga_clinical"), load_data("tcga_surv"), by
    = "sample"),
  opt_pancan = .opt_pancan
)

tcga_surv_plot(
  data,
  time = "time",
  status = "status",
  cutoff_mode = c("Auto", "Custom"),
  cutpoint = c(50, 50),
  cnv_type = c("Duplicated", "Normal", "Deleted"),
  profile = c("mRNA", "miRNA", "methylation", "transcript", "protein", "mutation", "cnv"),
  palette = "aaas",
  ...
)

Arguments

item

a molecular identifier, can be gene symbol (common cases), protein symbol, etc.

TCGA_cohort

a TCGA cohort, e.g. "LUAD" (default), "LUSC", "ACC".

profile

a molecular profile. Option can be one of "mRNA" (default), "miRNA", "methylation", "transcript", "protein", "mutation", "cnv".

TCGA_cli_data

a data.frame containing TCGA clinical data. Default use pre-compiled TCGA clinical data in this package.

opt_pancan

specify one dataset for some molercular profiles

data

a subset of result from tcga_surv_get().

time

the column name for "time".

status

the column name for "status".

cutoff_mode

mode for grouping samples, can be "Auto" (default) or "Custom".

cutpoint

cut point (in percent) for "Custom" mode, default is c(50, 50).

cnv_type

only used when profile is "cnv", can select from c("Duplicated", "Normal", "Deleted").

palette

color palette, can be "hue", "grey", "RdBu", "Blues", "npg", "aaas", etc. More see ?survminer::ggsurvplot.

...

other parameters passing to survminer::ggsurvplot

Value

a data.frame or a plot.

Examples

## Not run: 
# 1. get data
data <- tcga_surv_get("TP53")
# 2. filter data (optional)

# 3. show K-M plot
tcga_surv_plot(data, time = "DSS.time", status = "DSS")

## End(Not run)