Multivariate: TCGA Multivariate Analysis

In w2felix/TCGADataFelix: Analyzing the TCGA Data according to gene expression and survival

Description

TCGA Multivariate Analysis

Usage

Multivariate(x, Eset, value = 0, factor_list = F, mutation,
  average = "mean", optimal = FALSE, survival = "overall",
  return_df = FALSE, plot_cutpoint = F, coef = F, combined = F,
  stepwise = F, ...)

Arguments

x	A character vector with 1 or more gene names and/or columns of the clinical patient data
Eset	An Expression Set
value	Defines the value to subdivide gene expression groups. Numeric: Devided into two groups (for more genes use value = c(cutpoint gene 1, cutpoint gene 2, ...)) "q": 25 % quantile, 25-75 % quantile and 75 % quantile
factor_list	Returns the levels of factors in the analysis
mutation	Vector of mutations, that were added using the add_mutation() function
average	for more than one gene, how the value of the averaged z-score is calculated, either median or mean
optimal	calculate the optimal cutpoint, will overide the value value when numeric, does not work when value = "q"
survival	For overall survival = "overall", for disease free survival: survival = "DFS"
return_df	Returns the Dataframe that is used for calculatinf the Cox Regression
plot_cutpoint	Plot the graph how the optimal cutpoint was calculated, normal survival plot will be REPLACED by surv_cutpoint: Determine the optimal cutpoint for each variable using ’maxstat’
coef	Return the coefficients of the multivariate analysis instead of the multivariate object
combined	includes a comination of the different genes into the analysis. still in development
stepwise	Do a stepwise chosing a model by AIC to get rid of variables that don't play a role in the linear model
...	additional variables that can be added

Value

The summary of the multivariate analysis

Examples

## Not run: 
Multivariate(x = c("FOXA2", "GENDER"), Eset = Eset,
average = "median", stepwise=TRUE, coef=TRUE,
optimal=T, plot_cutpoint=F)

## End(Not run)

w2felix/TCGADataFelix documentation built on May 19, 2019, 8:24 a.m.