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b/man/compClinvar.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/compClinvar.R |
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\name{compClinvar} |
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\alias{compClinvar} |
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\title{Comparison of clinical variables} |
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\usage{ |
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compClinvar( |
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moic.res = NULL, |
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var2comp = NULL, |
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strata = NULL, |
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factorVars = NULL, |
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nonnormalVars = NULL, |
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exactVars = NULL, |
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includeNA = FALSE, |
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doWord = TRUE, |
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tab.name = NULL, |
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res.path = getwd(), |
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... |
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) |
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} |
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\arguments{ |
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\item{moic.res}{An object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms.} |
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\item{var2comp}{A data.frame of clinical variables that need to compare among current subtypes with rownames for samples and columns for variable names.} |
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\item{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.} |
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\item{factorVars}{A string vectors to indicate the categorical variables. If omitted, only factors are considered categorical variables.} |
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\item{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} |
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\item{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} |
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\item{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 \code{includeNA = T}. Only effective for categorical variables., Default: FALSE} |
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\item{doWord}{A logic value to indicate if transformating the .txt outfile to a .docx WORD file (.txt file will be also kept).} |
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\item{tab.name}{A string value to indicate the name of the output table.} |
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\item{res.path}{A string value to indicate the path for saving the table.} |
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\item{...}{Additionnal parameters pass to jstable::CreateTableOne2} |
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} |
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\value{ |
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A summarizing table with stastitical testing results. |
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} |
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\description{ |
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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. |
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} |
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\examples{ |
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# There is no example and please refer to vignette. |
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} |