knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
We illustrate the exact functional test with an example. An epigenetic indicator called CpG island methylator phenotype (CIMP) is strongly associated with liver cancers. Specimens [@shen2002dna] to study CIMP were collected and divided into three groups with different CIMP status: negative (no methylated genes), intermediate (1~2 methylated genes) and positive (>2 methylated genes).
The following table gives the frequencies of observed tumor protein p53 mutations and CIMP status:
Table: CpG Island Methylator Phenotype (CIMP) and p53 mutation.
CIMP CIMP CIMP
p53 mutation Negative Intermediate Positive -------------- ---------- -------------- ---------- No 12 26 18
Yes 0 8 12
require(FunChisq) # x is a contingency table with row variable for p53 mutation and # column variable for CIMP x <- matrix(c(12,26,18,0,8,12), nrow=2, ncol=3, byrow=TRUE) x # Test the functional dependency: p53 mutation -> CIMP res <- fun.chisq.test(x, method="exact") print(res) pval.text <- format.pval(res$p.value, digits=2) xif.text <- format.pval(res$estimate, digits=2) plot_table( x, xlab="CIMP", ylab="p53 mutation", col="seagreen3", main=bquote(italic(P)~'='~.(pval.text)*','~~italic(xi[f])~'='~.(xif.text)))
references: - id: shen2002dna title: DNA methylation and environmental exposures in human hepatocellular carcinoma author: - family: Shen given: L. - family: Ahuja given: N. - family: Shen given: Y. - family: Habib given: N. A. - family: Toyota given: M. - family: Rashid given: A. - family: Issa given: J.-P. J. container-title: Journal of the National Cancer Institute volume: 94 issue: 10 page: 755-761 type: article-journal issued: year: 2002 ...
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.