compClinvar: Comparison of clinical variables

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Create a table summarizing all baseline variables (both continuous and categorical) stratifying by current identified Subtypes and performing statistical tests. The object gives a table that is easy to use in medical research papers.

Usage

compClinvar(
  moic.res = NULL,
  var2comp = NULL,
  strata = NULL,
  factorVars = NULL,
  nonnormalVars = NULL,
  exactVars = NULL,
  includeNA = FALSE,
  doWord = TRUE,
  tab.name = NULL,
  res.path = getwd(),
  ...
)

Arguments

moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
var2comp	A data.frame of clinical variables that need to compare among current subtypes with rownames for samples and columns for variable names.
strata	A string value to indicate the stratifying variable. This function will generate an internal 'Subtype' variable which concatenates a string of 'CS' and values from 'clust' column of 'clust.res' in argument of ‘moic.res'. This argument is set as NULL by default and in this case using ’Subtype' variable as strata.
factorVars	A string vectors to indicate the categorical variables. If omitted, only factors are considered categorical variables.
nonnormalVars	A string vector to specify the variables for which the p-values should be those of nonparametric tests. By default all p-values are from normal assumption-based tests (oneway.test)., Default: NULL
exactVars	A string vector to specify the variables for which the p-values should be those of exact tests. By default all p-values are from large sample approximation tests (chisq.test)., Default: NULL
includeNA	A logic value to indicate if NA should be handled as a regular factor level rather than missing. NA is shown as the last factor level in the table if includeNA = T. Only effective for categorical variables., Default: FALSE
doWord	A logic value to indicate if transformating the .txt outfile to a .docx WORD file (.txt file will be also kept).
tab.name	A string value to indicate the name of the output table.
res.path	A string value to indicate the path for saving the table.
...	Additionnal parameters pass to jstable::CreateTableOne2

Value

A summarizing table with stastitical testing results.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.