Description Usage Arguments Details Value Author(s) References See Also Examples

Simple wrapper around stepAIC() (package MASS) to repeatedly perform stepwise model selection by AIC on several dependent variables (or responses, taken as rows of a matrix).

1 |

`y` |
Numeric matrix (with responses as rows and samples as columns) or ExpressionSet. Typically the expression data with transcripts (i.e. for a microarray, probes) as rows and samples as columns. If an ExpressionSet is provided the expression data is extracted with the function exprs. |

`subset` |
Integer vector. Represents a subset of samples (specified as column indices in y) to use for model fitting. By default all samples are used. |

`verbose` |
logical. If TRUE (default) the response number being fitted is printed. |

`upper` |
see ?stepAIC |

`lower` |
see ?stepAIC |

`direction` |
see ?stepAIC |

`trace` |
see ?stepAIC |

`keep` |
see ?stepAIC |

The initial model for the stepwise approach only contains an intercept term.

`swft` |
List of stepwise-selected models (see ?stepAIC) |

Alexandre Kuhn [email protected]

Kuhn A, Kumar A, Beilina A, Dillman A, Cookson MR, Singleton AB. Cell population-specific expression analysis of human cerebellum. BMC Genomics 2012, 13:610.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ```
## Load example expression data (variable "expression")
## and phenotype data (variable "groups")
data("example")
## Four cell population-specific reference signals
neuron_probesets <- list(c("221805_at", "221801_x_at", "221916_at"),
"201313_at", "210040_at", "205737_at", "210432_s_at")
neuron_reference <- marker(expression, neuron_probesets)
astro_probesets <- list("203540_at",c("210068_s_at","210906_x_at"),
"201667_at")
astro_reference <- marker(expression, astro_probesets)
oligo_probesets <- list(c("211836_s_at","214650_x_at"),"216617_s_at",
"207659_s_at",c("207323_s_at","209072_at"))
oligo_reference <- marker(expression, oligo_probesets)
micro_probesets <- list("204192_at", "203416_at")
micro_reference <- marker(expression, micro_probesets)
## Stepwise model selection for 2 transcripts (202429_s_at and 200850_s_at)
## and focusing on control samples (i.e. groups == 0)
swlm(expression[c("202429_s_at", "200850_s_at"),],
subset = which(groups == 0),
upper = formula(~neuron_reference + astro_reference +
oligo_reference + micro_reference))
``` |

PSEA documentation built on Nov. 17, 2017, 8:45 a.m.

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