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

In ChIPtest: Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-Seq Data

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 <[e-mail]> Maintainer: Vicky Qian Wu <[e-mail]>

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

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.