data1


In order to identify the genes that show differential histone modification levels between the two conditions, condition A and condition B, ChIPtest consider the upstream 5000 bp region and downstream 2000 bp region around the transcription start site (TSS) for each gene and divide the regions into 280 bins of 25 bps. Since the two ChIP-seq samples are usually sequenced at different depths (total number of reads), the counts were rescaled according to the sequencing depth ratio. In this example, suppose that there are 5 genes and for each gene, there are 280 observations. The input data matrix has 5 rows and 280 columns. Each row represents for one gene, and each column represents for number of short reads covered at one bin after rescaling. 


datasets

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.

Vicky Wu

ChIPtest

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

data1 function

The format is: num [1:5, 1:280] 0 0 0 0 1.43 0 1.43 0 0 1.43 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:5] "1" "2" "3" "4" ... ..$ : chr [1:280] "V3" "V4" "V5" "V6" ...

Format

T.S. Mikkelsen, et al. Comparative Epigenomic Analysis of Murine and Human Adipogenesis. Cell, 143 (156-169): 1156-1166 (2010)

data1: Input data (matrix) for condition A

Description

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Examples