methodsMerge: Integrate structural variations predicted by different...

In venyao/intansv: Integrative analysis of structural variations

Integrate structural variations predicted by different methods

Description

Integrate predictions of different tools to provide more reliable structural variations.

Usage

    methodsMerge(..., others=NULL, 
    overLapPerDel = 0.8, overLapPerDup = 0.8, overLapPerInv = 0.8,
    numMethodsSupDel = 2, numMethodsSupDup = 2, numMethodsSupInv = 2)

Arguments

...	results of different SVs predictions read in to R by intansv.
others	a data frame of structural variations predicted by other tools.
overLapPerDel	Deletions predicted by different methods that have reciprocal coordinate overlap larger than this threshold would be clustered together
overLapPerDup	Duplications predicted by different methods that have reciprocal coordinate overlap larger than this threshold would be clustered together
overLapPerInv	Inversions predicted by different methods that have reciprocal coordinate overlap larger than this threshold would be clustered together
numMethodsSupDel	Deletion clusters supportted by no more than this threshold of read support would be discarded
numMethodsSupDup	Duplication clusters supportted by no more than this threshold of read support would be discarded
numMethodsSupInv	Inversion clusters supportted by no more than this threshold of read support would be discarded

Details

A structural variation (deletion, duplication, inversion et al.) may be reported by different tools. However, the boundaries of this structural variation predicted by different tools don't always agree with each other. Predictions of different methods with reciprocal overlap more than 80 percent were merged. Structural varions supported by only one method were discarded.

Value

A list with the following components:

del	the integrated deletions of different methods.
dup	the integrated duplications of different methods.
inv	the integrated inversions of different methods.

Author(s)

Wen Yao

Examples

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

    cnvnator <- readCnvnator(system.file("extdata/cnvnator",package="intansv"))
    str(cnvnator)

    svseq <- readSvseq(system.file("extdata/svseq2",package="intansv"))
    str(svseq)

    delly <- readDelly(system.file("extdata/ZS97.DELLY.vcf",package="intansv"))
    str(delly)

    pindel <- readPindel(system.file("extdata/pindel",package="intansv"))
    str(pindel)

    sv_all_methods <- methodsMerge(breakdancer,pindel,cnvnator,delly,svseq)
    str(sv_all_methods)
    
    sv_all_methods.1 <- methodsMerge(breakdancer,pindel,cnvnator,delly,svseq,
                                 overLapPerDel=0.7)
    str(sv_all_methods.1)

    sv_all_methods.2 <- methodsMerge(breakdancer,pindel,cnvnator,delly,svseq,
                                 overLapPerDel=0.8, numMethodsSupDel=3)
    str(sv_all_methods.2)

venyao/intansv documentation built on Jan. 3, 2024, 6:15 p.m.