runBreakpointr: Wrapper function for breakpointR
In drashley/InversionAnalysis_HGSVC: Find breakpoints in Strand-seq data

Description Usage Arguments Details Author(s)

This script will move through .bam files in a folder and perform several steps (see Details).

runBreakpointr(input.data, dataDirectory = "./BreakPointR_analysis",
  pairedEndReads = TRUE, chromosomes = NULL, windowsize = 100,
  scaleWindowSize = T, trim = 10, peakTh = 0.33, zlim = 3.291,
  bg = 0.02, minReads = 20, writeBed = T, verbose = T)

`input.data`	A file with aligned reads in BAM format.
`dataDirectory`	Output directory. If non-existent it will be created.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`chromosomes`	If only a subset of the chromosomes should be processed, specify them here.
`windowsize`	The window size used to calculate deltaWs, either an integer or 'scale'.
`trim`	The amount of outliers in deltaWs removed to calculate the stdev (10 will remove top 10% and bottom 10% of deltaWs).
`peakTh`	The treshold that the peak deltaWs must pass to be considered a breakpoint.
`zlim`	The number of stdev that the deltaW must pass the peakTh (ensures only significantly higher peaks are considered).
`bg`	The amount of background introduced into the genotype test.
`minReads`	The minimum number of reads required for genotyping.
`writeBed`	If `TRUE`, will generate a bed of reads and deltaWs and breaks for upload onto the UCSC genome browser.
`verbose`	Verbose messages if `TRUE`.

1. calculate deltaWs chromosome-by-chromsome 2. localize breaks that pass zlim above the threshold 3. genotype both sides of breaks to confirm whether strand state changes 4. write a file of _reads, _deltaWs and _breaks in a chr fold -> can upload on to UCSC Genome browser 5. write a file for each index with all chromosomes included -> can upload on to UCSC Genome browser

Ashley Sanders, David Porubsky, Aaron Taudt

drashley/InversionAnalysis_HGSVC documentation built on May 6, 2019, 8:49 a.m.