Read in the structural variations predicted by CNVnator

Description

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

Usage

    readCnvnator(dataDir=".", regSizeLowerCutoff=100, regSizeUpperCutoff=1000000,
                 method="CNVnator")

Arguments

Details

The predicted SVs could be further filtered by the predicted size of SVs to get more reliable SVs. See our paper for more details. The directory that specified by the parameter "dataDir" should only contain the predictions of CNVnator. See the example dataset for more details.

Value

A list with the following components:

Author(s)

Wen Yao

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/readCnvnator.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readCnvnator
> ### Title: Read in the structural variations predicted by CNVnator
> ### Aliases: readCnvnator
> 
> ### ** Examples
> 
> 
>     cnvnator <- readCnvnator(system.file("extdata/cnvnator",package="intansv"))
>     str(cnvnator)
List of 2
 $ del:'data.frame':	369 obs. of  4 variables:
  ..$ chromosome: chr [1:369] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:369] 104101 230401 348301 1089301 1524301 ...
  ..$ pos2      : num [1:369] 110700 248400 350100 1103100 1529700 ...
  ..$ size      : num [1:369] 6599 17999 1799 13799 5399 ...
 $ dup:'data.frame':	113 obs. of  4 variables:
  ..$ chromosome: chr [1:113] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:113] 405001 973201 1346401 5036101 6419101 ...
  ..$ pos2      : num [1:113] 408900 977700 1359000 5055600 6423300 ...
  ..$ size      : num [1:113] 3899 4499 12599 19499 4199 ...
 - attr(*, "method")= chr "CNVnator"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>