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Last data update: 2014.03.03

R: Read in the structural variations predicted by Lumpy

readLumpy

R Documentation

Read in the structural variations predicted by Lumpy

Description

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

Usage

    readLumpy(file="", regSizeLowerCutoff=100, readsSupport=3, 
              method="Lumpy", regSizeUpperCutoff=1000000, 
              breakpointThres=200, scoreCut=0.1, ...)

Arguments

`file`	the file containing the prediction results of Lumpy.
`regSizeLowerCutoff`	the minimum size for a structural variation to be read.
`regSizeUpperCutoff`	the maximum size for a structural variation to be read.
`readsSupport`	the minimum read pair support for a structural variation to be read.
`method`	a tag to assign to the result of this function.
`breakpointThres`	a threshold to remove SVs with breakpoint with too large interval.
`scoreCut`	predictions with score larger than this threshold will be discarded.
`...`	parameters passed to read.table.

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:

`del`	the deletions predicted by Lumpy.
`dup`	the duplications predicted by Lumpy.
`inv`	the inversions predicted by Lumpy.

Author(s)

Wen Yao

Examples


    lumpy <- readLumpy(system.file("extdata/ZS97.lumpy.pesr.bedpe",package="intansv"))
    str(lumpy)

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/readLumpy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readLumpy
> ### Title: Read in the structural variations predicted by Lumpy
> ### Aliases: readLumpy
> 
> ### ** Examples
> 
> 
>     lumpy <- readLumpy(system.file("extdata/ZS97.lumpy.pesr.bedpe",package="intansv"))
>     str(lumpy)
List of 3
 $ del:'data.frame':	1047 obs. of  4 variables:
  ..$ chromosome: chr [1:1047] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:1047] 65582 86450 201842 208220 230514 ...
  ..$ pos2      : num [1:1047] 65936 87424 201976 208548 230656 ...
  ..$ size      : num [1:1047] 355 975 134 329 142 ...
 $ dup:'data.frame':	37 obs. of  4 variables:
  ..$ chromosome: chr [1:37] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:37] 910606 957196 1133966 1615004 5757302 ...
  ..$ pos2      : num [1:37] 911322 957324 1136616 1616026 5758086 ...
  ..$ size      : num [1:37] 717 127 2650 1023 784 ...
 $ inv:'data.frame':	47 obs. of  4 variables:
  ..$ chromosome: chr [1:47] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:47] 2088840 3277686 5899568 6372408 6613076 ...
  ..$ pos2      : num [1:47] 2089006 3278456 5899762 6453738 6645398 ...
  ..$ size      : num [1:47] 166 770 194 81331 32323 ...
 - attr(*, "method")= chr "Lumpy"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>