dipPeaks: Estimate density and find peaks

Description Usage Arguments Examples

Description

Calculates a smoothed track from input count data, and identifies peaks in the data. Outputs the peaks and smoothed track to file.

Usage

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dipPeaks(bamFile, bigWigOut = NULL, chromInfo = NULL,
  scratchDirBase = "~", outDir = "~", kernel = "e", cores = 1,
  perChromCutoff = FALSE, windowSize = 50, windowStep = 5,
  indexFile = NULL, retainTemp = FALSE, limitChrom = NULL)

Arguments

bamFile

Input file in bam format

bigWigOut

Produce a smoothed output density file in bigwig format (using wigToBigWig)?

chromInfo

UCSC chromInfo.txt file (required only for bigWigOut)

scratchDirBase

Directory for scratch output; use local disk for optimal processing. dipPeak writes a significant amount of data to disk as it runs, to reduce memory use. This I/O takes time, and will be faster if you use a local disk or fast mount spot.

outDir

Final folder (the files to keep will be moved here from the scratch dir).

kernel

'e' for Epanechinov; 'g' for Gaussian; 'm' for Mexican Hat

cores

Add additional cores (up to 23) for faster processing. (Default:1)

perChromCutoff

Boolean; If yes, calculates a per-chromosome; otherwise, defaults to genome-wide cutoff.

windowSize

Choose the size of the smoothing window (default:50)

windowStep

Choose the window step (5 will take a window every 5 bases) (default:5)

indexFile

Index file made from "samtools index" on the bam input file; deaults to bamFile.bai, or you can provide one.

retainTemp

Do you want to retain temporary files?

limitChrom

You can limit the smoothing to a list of chromosomes (defaults to everything in the bam file)

Examples

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dipPeaks("sequences.bam", bigWigOut="density.bw", outDir="outDir", cores=8);

nsheff/dipPeak documentation built on May 24, 2019, 7:50 a.m.