est.c {ChIPtest}

R Documentation

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

Description

If there is no INPUT experiment (No control), treat the genes with read counts fewer than 5 as the "null genes". Test statistics were calculated based on the those "null genes" and take the average to obtain the value c, which is used in the null hypothesis H0: TS=c

Usage

est.c(data1, data4, max1 = 5, max4 = 5)

Arguments

data1	Data Matrix (after VST) for condition A
data4	Data Matrix (after VST) for condition B
max1	Threshold used to decide null genes for condition A. Default as 5
max4	Threshold used to decide null genes for condition B. Default as 5

Details

Data matrix, the default format is N row by M column. Each row represents for one gene, and each column represents for one bin

Value

tao	value c in the null hypothesis H0: TS=c

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)

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