Chipseq_Peak_demo

datasets

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

Xinan Yang  with contribution from Lorenzo Pesce lpesceuchicagoedu

seq2pathway

a novel tool for functional gene-set (or termed as pathway)
analysis of next-generation sequencing data

Chipseq_Peak_demo function

A data frame with 5 observations on the following 5 variables.
  <dl>
    <dt><code>peakID</code></dt><dd>unique chip peak name information</dd> <dt><code>chrom</code></dt><dd>chromosome information</dd> <dt><code>start</code></dt><dd>loci start</dd> <dt><code>end</code></dt><dd>loci end</dd> <dt><code>signalvalue</code></dt><dd>a numeric vector</dd> </dl> 

Chipseq_Peak_demo: chip seq loci data example

Description

Usage

Arguments

Value

Format

Examples