Description Usage Arguments Value Author(s) References Examples

This is a wrapper function for MAP-Matches method.

1 | ```
MAP.Matches(data, varname, t.cutoff = "98.00%", multiple = TRUE, perm = c("both", "columns", "labels")[1], nperm = 1000, test = c("t", "t.equalvar")[1], sig.col, sig.cutoff = 0.05)
``` |

`data` |
Object of class |

`varname` |
Character String - name of one column in clinical data matrices to be used as class labels |

`t.cutoff` |
Character String - quantile of T statistics to be selected, e.g. "95.00%" selects the top 5 percent of absolute values |

`multiple` |
Logical - when |

`perm` |
Character String - if |

`nperm` |
Numeric - number of permutations |

`test` |
Character String - if |

`sig.col` |
Character String - which p-value is used for selection of significant patterns. Possible values are: |

`sig.cutoff` |
Numeric - p-value for selection of sigificant patterns |

Object of class `MAP.Matches.res`

containing

`tests ` |
Data.frame of test statistics |

`bin.matrix` |
Binary matrix from |

`sumarization` |
Sumarization of |

`MAP ` |
Data frame describing observed patterns: number of strong |

`stat.analysis` |
Results of statistical analysis |

`genes` |
List of genes observed with each pattern |

`all.genes` |
Names of the all genes in the analysis |

Ivana Ihnatova

Yang, X., Bentink, S. and Spang, R. 2005, Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities, Biomedical Microdevices, Vol.7:3, pp. 247-251

1 2 | ```
data(ColonData)
MAP.Matches(ColonData, "MSI", nperm = 100, sig.col="p.lab.strong")
``` |

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