Description Usage Arguments Details Value Author(s) Examples

Peform POST analysis with linear model

1 2 |

`exprSet` |
an ExpressionSet class contains minimum of exprs (expression matrix) of genomic data such as gene expression and phenoData (AnnotatedDataFrame of end point data). Please refer to Biobase for details on how to create such an ExpressionSet expression set. |

`geneSet` |
a GeneSetCollection class with minimum of setName and geneIDs for each GeneSet.
Please refer to |

`lamda` |
a predefined fraction of 0 to 1: the fraction of variation retained in the selected orthogonal projections |

`seed` |
seed of random number generator |

`nboots` |
number of bootstrap samples, default=100 |

`model` |
a character string to define the model |

`family` |
a description of the error distribution and link function to be used in the model. For glm, this can be a character string naming a family function, a family function or the result of a call to a family function. |

`...` |
control arguments to be passed to generalized linear model, default control argument are used if they are not supplied directly |

The function performs POST analysis for association of gene sets with phenotype in generalized linear model framework.

a data frame with 5 columns

`GeneSet` |
Gene set id |

`Nprobe` |
numbe of probes in the ExpressionSet annotated to the gene set |

`Nproj` |
number of projected vectors included in the POST analysis |

`Stat` |
statistic of quadratic form |

`p.value` |
p value of generalized Chi-square approximation |

Xueyuan Cao Xueyuan.cao@stjude.org, Stanley Pounds stanley.pounds@stjude.org

1 2 3 4 5 6 7 8 9 10 11 | ```
## load data
data(sampExprSet)
data(sampGeneSet)
test<-POSTglm(exprSet=sampExprSet,
geneSet=sampGeneSet,
lamda=0.95,
seed=13,
nboots=100,
model='Group ~ ',
family=binomial(link = "logit"))
``` |

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