visGenotypeComparison: This function runs statistical analysis (wilcoxon test) which...

In kkolmus/MolecularAnalyzeR: This package aims at checking correlation between gene expression and copy number variation for cohorts of patients analyzed within The Cancer Genome Atlas project

Description

This function runs statistical analysis (wilcoxon test) which aims at finding differences between expression of gene 2 among copy number variations of gene 1.

Usage

visGenotypeComparison(
  data,
  gene1,
  gene2,
  method = c("log", "rlog", "vst"),
  threshold = 10
)

Arguments

data	output of the prepareData function
gene1	gene for which copy number data were extracted, character string
gene2	gene for which normalized expression data were extracted, character string
method	method used for expression data normalization log = log2(count+1), rlog = regularized log transformation, vst = variance stabilizing transformation
threshold	minimal number of patients to visualize results

Value

boxplot

Examples

## Not run: visualizeGenotypeComparison(data,
                                     gene1 = "CDK11A",
                                     gene2 = "CFLAR",
                                     method = "vst",
                                     threshold = 10)
## End(Not run)

kkolmus/MolecularAnalyzeR documentation built on Dec. 21, 2021, 6:46 a.m.