Description Arguments Details Value References See Also Examples

'getsGLA' is used to calculate the sGLA test statistic and correponding p value.

`object` |
An numerical matrix object with three columns or an object of ExpresionSet class with three features. |

`boots` |
The number of bootstrap iterations for estimating the bootstrap standard error of sGLA. Default value is boots=30. |

`perm` |
The number of permutation iterations for generating the null distribution of the sGLA test statistic. Default is perm=100. |

`cut` |
cut==M +1. M is the number of grip points pre-specifed over the third variable. |

`dim` |
An index of the column for the gene to be treated as the third controller variable. Default is dim=3 |

`geneMap` |
A character vector with three elements representing the mapping between gene names and feature names (optional). |

The input object can be a numerical matrix with three columns with row representing observations and column representing three variables. It can also be an ExpressionSet object with three features. If input a matrix class data, all three columns of the object representing the variables should have column names. Each variable in the object will be standardized with mean 0 and variance 1 in the function. In addition, the third variable will be quantile normalized within the function. More detail example about the usage of geneMap is demonstrated in the vignette.

'getsGLA' returns a vector with two elements. The first element is the value of test statistic and second element is the corresponding p value. A more detailed interpretation of these values is illustrated in the vignette.

Yen-Yi Ho, Leslie Cope, Thomas A. Louis, and Giovanni Parmigiani, GENERALIZED LIQUID ASSOCIATION (April 2009). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 183. http://www.bepress.com/jhubiostat/paper183.

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