readBreakDancer: Read in the structural variations predicted by breakDancer
In intansv: Integrative analysis of structural variations

Description Usage Arguments Details Value Author(s) Examples

Reading in the structural variations predicted by breakDancer, filtering low quality predictions and merging overlapping predictions.

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    readBreakDancer(file="", scoreCutoff=60, readsSupport=3, 
                    regSizeLowerCutoff=100, regSizeUpperCutoff=10000000,
                    method="BreakDancer", ...)

`file`	the output file of breakDancer.
`scoreCutoff`	the minimum score for a structural variation to be read in.
`readsSupport`	the minimum read pair support for a structural variation to be read in.
`regSizeLowerCutoff`	the minimum size for a structural variation to be read in.
`regSizeUpperCutoff`	the maximum size for a structural variation to be read in.
`method`	a tag to assign to the result of this function.
`...`	parameters passed to read.table.

The predicted SVs could be further filtered by score, number of read pairs supporting the occurence of a specific SV, and the predicted size of SVs to get more reliable SVs. See our paper for more details.

A list with the following components:

`del`	the deletions predicted by breakDancer.
`inv`	the inversions predicted by breakDancer.

Wen Yao

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    breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
                                   package="intansv"))
    str(breakdancer)