runBreakpointr {breakpointR} | R Documentation |
Find breakpoints in Strand-seq data. See section Details on how breakpoints are located.
runBreakpointr(bamfile, ID = basename(bamfile), pairedEndReads = TRUE, chromosomes = NULL, windowsize = 1e+06, binMethod = "size", trim = 10, peakTh = 0.33, zlim = 3.291, background = 0.05, min.mapq = 10, pair2frgm = FALSE, filtAlt = FALSE, genoT = "fisher", minReads = 20, maskRegions = NULL, conf = 0.99)
bamfile |
A file with aligned reads in BAM format. |
ID |
A character string that will serve as identifier in downstream functions. |
pairedEndReads |
Set to |
chromosomes |
If only a subset of the chromosomes should be binned, specify them here. |
windowsize |
The window size used to calculate deltaWs, either number of reads or genomic size depending on |
binMethod |
Method used to calculate optimal number of reads in the window ("size", "reads"). By default |
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 (e.g. 0.33 is 1/3 of max(deltaW)). |
zlim |
The number of stdev that the deltaW must pass the peakTh (ensures only significantly higher peaks are considered). |
background |
The percent (e.g. 0.05 = 5%) of background reads allowed for WW or CC genotype calls. |
min.mapq |
Minimum mapping quality when importing from BAM files. |
pair2frgm |
Set to |
filtAlt |
Set to |
genoT |
A method ('fisher' or 'binom') to genotype regions defined by a set of breakpoints. |
minReads |
The minimal number of reads between two breaks required for genotyping. |
maskRegions |
List of regions to be excluded from the analysis (tab-separated file: chromosomes start end). |
conf |
Desired confidence interval of localized breakpoints. |
Breakpoints are located in the following way:
calculate deltaWs chromosome-by-chromsome
localize breaks that pass zlim above the threshold
genotype both sides of breaks to confirm whether strand state changes
write a file of _reads, _deltaWs and _breaks in a chr fold -> can upload on to UCSC Genome browser
write a file for each index with all chromosomes included -> can upload on to UCSC Genome browser
A BreakPoint
object.
David Porubsky, Ashley Sanders, Aaron Taudt
## Get an example file exampleFolder <- system.file("extdata", "example_bams", package="breakpointRdata") exampleFile <- list.files(exampleFolder, full.names=TRUE)[1] ## Run breakpointR brkpts <- runBreakpointr(exampleFile, chromosomes='chr22', pairedEndReads=FALSE)