ChIPtest (version 1.0)

TS_twosample: Three Nonparametric Test Statistics for two sample ChIP-seq data

Description

It includes three nonparametric test statistics for two sample differential analysis: kernel based nonparametric test, assumption-free nonparametric test with equal variance estimation and unequal variance estimation.

Usage

TS_twosample(data1, data4, tao, band, quant)

Arguments

data1

data matrix (after VST) for condition A

data4

data matrix (after VST) for condition B

tao

the biologically relevant value c in the null hypothesis H0: TS=c, in assumption-free nonparametric test

band

bandwidth used in kernel smoothing

quant

threshold used in variance estimation

Value

Details

kernel-based test statistics is the same as "TS_kernel"

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))