narrowpeaksDiff: Differential Analysis of Transcription Factor Binding using...

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

Description

Shape-based differential binding analysis and hypothesis testing for ChIP-seq datasets using Functional Principal Component Analysis and Hotelling's T2 tests.

Usage

narrowpeaksDiff(bedFile,  headerBed= TRUE, flank=100, bigwigs , conditions , 
nbasis=50, pcs = 10, bigWigSummaryPath=getwd(), variation = 0.6)

Arguments

bedFile	Text file in BED format. It should contain at least 3 columns (chr, start, end), in which case the reference point for FDA is calculated as the central point. A 4-th column can be provided containing the reference point.
headerBed	'TRUE' if the first row in the BED file contain the name of the columns. 'FALSE' otherwise.
flank	Length (in bp.) that is considered upstream and downstream the reference point (or central point, if reference point is not given) for functional principal component analysis.
bigwigs	Vector contaning the name of the bigWig files to be used in the analysis.
conditions	Vector of characters with the LABELS for the bigWig files. Biological replicates must have the same label.
nbasis	Number of order-4 B-Spline basis functions for functional data analysis.
pcs	Number of principal components to be computed (default is 10).
bigWigSummaryPath	Path to the UCSC utility bigWigSummary (in case it is differente from the current directory). The tool can be downloaded for Linux and macOSX from the UCSC website: http://hgdownload.cse.ucsc.edu/admin/exe/
variation	Minimum proportion of variation that is considered to select the number of functional principal component scores used in the Hotelling's T2 tests (0-1, default is 0.6).

Details

Detailed information can be found in the vignette of the package.

Value

A list containing the following elements:

fdaprofiles	A list of matrices corresponding to the data of regions of interest (BED file) in the bigWig files.
p.values	A list of pairwise comparisons between experimental conditions (taking into account replicates) for each region in the BED file. P-values are computed using the Hotelling's T2 test.

Author(s)

Pedro Madrigal, [e-mail]

References

Mateos JL, Madrigal P, et al. (2015) Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology 16: 31.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq data. PLOS Comput Biol. 9 (11): e1003326.
Ramsay, J.O. and Silverman, B.W. (2005) Functional Data Analysis. New York: Springer.

See Also

narrowpeaks, NarrowPeaks-package

Examples

##Example code:
##library(NarrowPeaks)
##bigwigs <- c("SVP_WT_rep1.bw","SVP_WT_rep2.bw","SVP_WT_rep3.bw",
## "SVP_mt_rep1.bw","SVP_mt_rep2.bw","SVP_mt_rep3.bw")
##conds   <- c("SVP_WT","SVP_WT","SVP_WT","SVP_mt","SVP_mt","SVP_mt")
##x <- narrowpeaksDiff(bedFile="regions.bed", bigwigs=bigwigs, conditions=conds, variation = 0.8)
##x$p.values

NarrowPeaks documentation built on April 28, 2020, 6:51 p.m.