View source: R/rejectionPlot.R

rejectionPlot | R Documentation |

This function plots the observed and expected numbers of rejected tests and their ratio as a function of alpha.

rejectionPlot(X,lCol="red",xlim=NULL,crit=NULL,rejLine = NULL, alpha = 0.01, rej.lty = c("dotted"), rej.col = "black", incLegend=NULL)

`X` |
Matrix or vector of p-values, as obtained from |

`lCol` |
Vector of of line colors |

`xlim` |
An interval for alpha values (for the plotting). Default is [0,1]. |

`crit` |
Shall the distance or the ratio be plotted, see details. |

`rejLine` |
Type of rejection line. Options are |

`alpha` |
Alpha for the multiple testing adjusted p-value- determines the slope of the rejection line. |

`rej.lty` |
Line type of the rejection line. |

`rej.col` |
Colour of the rejection line. |

`incLegend` |
Position of a possible legend. |

The matrix `X`

contains p-values as given from the `gmw`

function. The rows correspond to different tests,
and the columns to different variables.

The function plots, for each test separately, the observed and expected numbers of rejected tests and their ratio (`crit="ratio"`

)
or distance (`crit="distance"`

) as a function of alpha.

Daniel Fischer

Fischer, D., Oja, H., Schleutker, J., Sen, P.K., Wahlfors, T. (2013): Generalized Mann-Whitney Type Tests for Microarray Experiments, Scandinavian Journal of Statistic, to appear.

Fischer, D., Oja, H. (2013): Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT, submitted article.

`gmw`

X <- matrix(c(rnorm(50,2,1),rnorm(60,2,1),rnorm(40,2.5,1)),byrow=TRUE, ncol=10) colnames(X) <- letters[1:10] g <- c(rep(1,5),rep(2,6),rep(3,4)) test1 <- gmw(X,g,test="mw",type="external",alternative="greater",goi=c(2,3)) test2 <- gmw(X,g,test="kw",type="external") test3 <- gmw(X,g,test="jt",type="external",alternative="greater") tests <- rbind(test1$p.values,test2$p.values,test3$p.values) rejectionPlot(tests,lCol=c("green","red","blue"))

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