Description Usage Arguments Details Value References Examples

Get the difference between two conditions. Apply Kernel smoothing to fit a smooth curve. Estimate variance for each gene and improve the estimation of variance based on all the genes. Derive test statistics and get the rank list of all the genes.

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`data` |
difference matrix between two conditions |

`band` |
bandwidth used in kernel smoothing |

`quantile` |
threshold used in variance estimation |

Note 1: Need to chose a bandwidth. Do not recommend to use cross validation (not gene-specific bandwidth) but chose a fixed biological meaningful bandwidth. A fixed bandwidth which can capture the signal profile and smooth out noise would be recommend. The bandwidth used in reference is 20/280.

Note 2: quantile value is based on the distribution of variance estimation of each gene. Recommend to use histogram to double check the distribution. Default 0.9 = 90 %

`TS ` |
Kernel based test statistics after WH transformation. Please refer the details in the reference |

`TS_sign ` |
"+" represent for condition B enriched more than condition A; "-" vice versa |

`Tmean ` |
Original test statistics, which is calculated as integral of square of kernel estimator |

Qian Wu, Kyoung-Jae Won and Hongzhe Li. (2015) Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-seq Data. *Cancer Informatics*,14 (Suppl 1), 11-22

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