ChIPtest-package: Nonparametric Methods for Identifying Differential Enrichment...

Description Details Author(s) References Examples

Description

Nonparametric Tests to identify the differential enrichment region for two conditions or time-course ChIP-seq data. It includes: data preprocessing function, estimation of a small constant used in hypothesis testing, a kernel-based two sample nonparametric test, two assumption-free two sample nonparametric test.

Details

Package: ChIPtest_1.0
Type: Package
Version: 1.0
Date: 2016-07-07
License: GPL ( >=2
LazyLoad: yes

Author(s)

Vicky Qian Wu ; Kyoung-Jae Won ; Hongzhe Li <hongzhe@upenn.edu> Maintainer: Vicky Qian Wu <wuqian7@gmail.com>

References

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

Examples

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data(data1)
data(data4)
Data1=NormTransformation(data1)
Data4=NormTransformation(data4)
tao=est.c(Data1, Data4, max1=5, max4=5)
band=54
TS=TS_twosample(Data1, Data4, tao, band, quant=c(0.9,0.9,0.9))

Example output

Warning message:
In TS_twosample(Data1, Data4, tao, band, quant = c(0.9, 0.9, 0.9)) :
  imaginary parts discarded in coercion

ChIPtest documentation built on May 2, 2019, 3:37 p.m.