pipe.ChIPpeaks: Turn Alignments into Wiggle Tracks and ChIP Peaks.

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Turn Alignments into Wiggle Tracks and ChIP Peaks.

Description

Pipeline step that generates files of ChIP peaks for one sample. The alignment BAM files are converted to strand specific and unique/multi-hit wiggle tracks, and then the read pileup depth is interogated for the presence of ChIP peaks.

Usage

pipe.ChIPpeaks(sampleID, annotationFile = "Annotation.txt", optionsFile = "Options.txt", 
	speciesID = NULL, results.path = NULL, loadWIG = FALSE, storage.mode = "normal", 
	doPeakSearch = TRUE, peak.type = "auto", cutoff.medians = 3, canonical.width = 50, 
	use.multicore = TRUE, p.value = 0.25, verbose = FALSE, 
	watermark.gene = sub("_[BS][0-9]+$", "", sampleID), 
	controlPeaksFile = NULL, scaledReadCount = NULL, visualize = interactive())

Arguments

sampleID	The SampleID for this sample. This SampleID keys for one row of annotation details in the annotation file, for getting sample-specific details. The SampleID is also used as a sample-specific prefix for all files created during the processing of this sample.
annotationFile	File of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.
optionsFile	File of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
speciesID	The SpeciesID of the target species to calculate a transcriptome for. By default, transcriptome for all species in the current target are generated.
results.path	The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.
loadWIG	Logical, should all wiggle track data structures be rebuilt from the alignment BAM files. By default, the wiggle files are only created if they do not yet exist for this sample.
storage.mode	Controls the behavior of how alignments are loaded into the the wiggle track data objects.
doPeakSearch	Logical, controls whether the full peak search algorithm is run, or to instead just rerun the post-search summarization and plotting steps of this pipeline.
peak.type	Controls the type of peak shapes the picker evaluates against the raw pileup data. Choices are 'gaussian', 'gumbel', 'lorentz', and 'auto'. The default 'auto' lets the peak picker use all known peak shapes and select the one that best fits the raw data at each location.
cutoff.medians	Defines the cutoff threshold between noise and potential true peaks, as a multiple of the strand's median raw read pileup depth. Only locations having higher read depth than the cutoff threshold will be passed to the lower level peak picking algorithm. Setting the cutoff too low will slow computation and introduce false peaks, while setting it too high will cause some true but smaller peaks to be missed.
canonical.width	Used to define the canonical 'half-width at half-height' (HWHH) of an expected ChIP peak in the sample. As the ChIP peaks themselves are a result of read pileups at various locations along the genome, the best starting estimate for the canonical width will be exactly the length in nucleotides of the raw reads in the FASTQ data.
use.multicore	Logical, should the three strands of raw read pileup data (forward, reverse, and combined) be run in parallel as three separate child peakpick processes. As of R version 3, plotting during multicore is no longer supported, so care should be taken with this argument.
p.value	The limiting P-value for determining how many peaks to include in the final tables of ChIP peak results. Peaks with poor scoring final P-values are omitted.
verbose	Logical, send progress information to standard out.
watermark.gene	The GeneID of the induced gene for this sample. In some experiments, we expect an overabundance of read pileup data at the induced gene. The algorithm does a extra step of median subtraction inside the gene boundary prior to peak search, to help deconvolute the induction artifact from any true ChIP peak in the area of the gene. Set to 'NULL' to disable this behavior.
controlPeaksFile	Character filename of a set of negative control peaks from samples that should not have real ChIP peaks. This set of 'non-peaks' are used for calculating the P-values for peaks in the given sample.
scaledReadCount	Total raw read count that all samples will be scaled to prior to peak picking, to assure that all samples will be scored in an equivalent manner. Many of the peak shape scoring metrics are influenced by read depth, so this helps give uniform peak scoring between samples.
visualize	Logical, should the pipeline generate plot images of peak evaluation and final peak calls during the peak search run. Plotting can only occur in an interactive session. Assumes the program is running on a machine that supports X11 graphics.

Details

This is the high level pipeline step for finding ChIP peaks in a sample. If needed, it first turns the BAM alignments into wiggle track data; then calls the peak peaker, and finally generates several files of ChIP peak results.

The algorithm was written and tuned for the transcription factor induction data from Minch & Rustad (DOI: 10.1038/ncomms6829) of M.tuberculosis. It may need some retuning for other genomes and/or sequencing data variabilities.

Value

A family of files are written to this sample's subfolder in the 'ChIPpeaks' folder of results. These include:

Strand specific peak files	Three text files of single strand peak calls, for the forward, reverse, and combined wiggle tracks.
Strand specific ROC curve plots	If interactive graphics were generated, ROC curves of the peak pick score distributions are made.
Final peaks text file	One text file of final peak calls, after combining the 3 strand-specific results to find peak triplets that satisfy the properties of a true ChIP peak.
Final peaks .csv file	One Excel readable file of final peak calls, after appending a column of the genomic DNA sequence under the peak. This column is configured as FASTA sequences that can be submitted to a motif detection algorithm to find the binding motif of that sample's transcription factor.
Final peaks .html file	One web browser readable file of final peak calls, with hyperlinks into a subfolder of plot images of all final ChIP peaks.
Peaks scoring details	One text file of all scoring metric details for all identified peaks. Useful for tuning the algorithm or just understanding why peaks got scored as they did.

Author(s)

Bob Morrison

References

The DNA-binding network of Mycobacterium tuberculosis KJ Minch, TR Rustad, et.al. Nature Communications 6, Article number: 5829, doi:10.1038/ncomms6829

See Also

calcWigChIPpeaks for the intermediate level implementation, and findPeaks for the low level single strand read pileup depth peak pick tool.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.