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Last data update: 2014.03.03

R: Read in the structural variations predicted by Pindel

readPindel

R Documentation

Read in the structural variations predicted by Pindel

Description

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

Usage

    readPindel(dataDir=".", regSizeLowerCutoff=100, 
               regSizeUpperCutoff=1000000, readsSupport=3,
               method="Pindel")

Arguments

`dataDir`	the directory containing the prediction results of Pindel.
`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.

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. The directory that specified by the parameter "dataDir" should only contain the predictions of Pindel. The deletions output files should be named using the suffix "_D", the duplications output files should be named using the suffix "_TD", and the inversions output files should be named using the suffix "_INV". See the example dataset for more details.

Value

A list with the following components:

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

Author(s)

Wen Yao

Examples


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

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/readPindel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readPindel
> ### Title: Read in the structural variations predicted by Pindel
> ### Aliases: readPindel
> 
> ### ** Examples
> 
> 
>     pindel <- readPindel(system.file("extdata/pindel",package="intansv"))
>     str(pindel)
List of 3
 $ del:'data.frame':	677 obs. of  4 variables:
  ..$ chromosome: chr [1:677] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:677] 76477 86438 120431 334346 366428 ...
  ..$ pos2      : num [1:677] 76913 87419 127842 334613 367941 ...
  ..$ size      : num [1:677] 435 980 7410 266 1512 ...
 $ inv:'data.frame':	52 obs. of  4 variables:
  ..$ chromosome: chr [1:52] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:52] 777580 1385804 2580617 3062624 6298321 ...
  ..$ pos2      : num [1:52] 777810 1390029 2583765 3062746 6311292 ...
  ..$ size      : num [1:52] 229 4224 3147 121 12970 ...
 $ dup:'data.frame':	68 obs. of  4 variables:
  ..$ chromosome: chr [1:68] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : num [1:68] 97139 120110 910586 957199 1018140 ...
  ..$ pos2      : num [1:68] 97308 127734 911325 957324 1018273 ...
  ..$ size      : num [1:68] 168 7623 738 124 132 ...
 - attr(*, "method")= chr "Pindel"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>