Read in the structural variations predicted by SoftSearch

Description

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

Usage

    readSoftSearch(file="", regSizeLowerCutoff=100, readsSupport=3, 
                   method="softSearch", regSizeUpperCutoff=1000000, 
                   softClipsSupport=3, ...) 

Arguments

Details

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

Value

A list with the following components:

Author(s)

Wen Yao

Examples

    softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv"))
    str(softSearch)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(intansv)
Loading required package: plyr
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:plyr':

    rename

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:plyr':

    desc

Loading required package: GenomeInfoDb
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/intansv/readSoftSearch.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSoftSearch
> ### Title: Read in the structural variations predicted by SoftSearch
> ### Aliases: readSoftSearch
> 
> ### ** Examples
> 
> 
>     softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv"))
>     str(softSearch)
List of 3
 $ del:'data.frame':	47 obs. of  4 variables:
  ..$ chromosome: chr [1:47] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:47] 366291 1491176 1802871 2986918 14116786 ...
  ..$ pos2      : num [1:47] 367937 1491595 1803476 2987435 14129776 ...
  ..$ size      : num [1:47] 1646 419 605 517 12990 ...
 $ dup: NULL
 $ inv:'data.frame':	4 obs. of  4 variables:
  ..$ chromosome: chr [1:4] "chr05" "chr05" "chr10" "chr10"
  ..$ pos1      : num [1:4] 3106094 18770855 2460956 7020583
  ..$ pos2      : num [1:4] 3106380 19669803 2512674 7021271
  ..$ size      : num [1:4] 286 898948 51718 688
 - attr(*, "method")= chr "softSearch"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>