wigfile_test

NarrowPeaks-dataset

Example of wiggle track produced after ChIP-seq data analysis. The 
data represents a small subset of a WIG file storing continuous-valued scores 
 based on a Poisson test for the chromosome 1 of Arabidopsis thaliana 
(Kaufmann et al., 2010). It contains first 49515 lines of the WIG file for the
 complete experiment.

datasets

The package applies a functional
version of principal component analysis (FPCA) to: (1) Postprocess
data in wiggle track format, commonly produced by generic ChIP-seq
peak callers, by applying FPCA over a set of read-enriched
regions (ChIP-seq peaks). This is done to study variability of the
the peaks, or to shorten their genomic
locations accounting for a given proportion of variation among
the enrichment-score profiles. (2) Analyse
differential variation between multiple ChIP-seq samples with
replicates. The function 'narrowpeaksDiff' quantifies differences
between the shapes, and uses Hotelling's T2 tests on
the functional principal component scores to identify
significant differences across conditions. An application of the package
for Arabidopsis datasets is described in Mateos, Madrigal, et al.
(2015) Genome Biology: 16:31.

Pedro Madrigal

NarrowPeaks

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

wigfile_test function

Wiggle track format (WIG) data in a character vector.

Format

Gene Expression Omnibus GSE20176 
(<a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20176">http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20176</a>). Record from
 chromatin immunoprecipitation experiments wit AP1-specific antibodies followed
 by deep-sequencing in order to determine AP1 binding sites on a genome-wide 
scale in Arabidopsis thaliana.

Source

Example of wiggle track produced after ChIP-seq data analysis. The 
data represents a small subset of a WIG file storing continuous-valued scores 
 based on a Poisson test for the chromosome 1 of Arabidopsis thaliana 
(Kaufmann et al., 2010). It contains first 49515 lines of the WIG file for the
 complete experiment.

wigfile_test: Example Wiggle Track Produced After ChIP-seq Data Analysis

Description

Arguments

Format

Source

References

See Also