Choose fragments in a provided region around the viewpoint

Description

This function extracts fragment data from a Data4Cseq object's rawFragments slot for visualization with the functions visualizeViewpoint and drawHeatmap . Relevant fragments are located within the chosen visualization range; the viewpoint itself can be excluded or included.

Usage

chooseNearCisFragments(expData, regionCoordinates, deleteViewpoint = TRUE)

Arguments

Value

A data frame containing the chosen near-cis fragments

Note

Viewpoint fragments are removed per default to prevent bias through overrepresented sequences caused by self-ligation. These fragments can be included, but should be interpreted with caution.

Author(s)

Carolin Walter

Examples

  # read example data
  data(liverData)
  fragments<-chooseNearCisFragments(liverData, regionCoordinates = c(20800000, 21000000))
  head(fragments)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Basic4Cseq)
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

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

    runmean

The following object is masked from 'package:S4Vectors':

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/chooseNearCisFragments.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chooseNearCisFragments
> ### Title: Choose fragments in a provided region around the viewpoint
> ### Aliases: chooseNearCisFragments
> ###   chooseNearCisFragments,Data4Cseq,numeric-method
> ### Keywords: chooseNearCisFragments
> 
> ### ** Examples
> 
>   # read example data
>   data(liverData)
>   fragments<-chooseNearCisFragments(liverData, regionCoordinates = c(20800000, 21000000))
>   head(fragments)
    chromosomeName fragmentStart fragmentEnd fragmentCentre isNonBlind
104             10      20803166    20804714       20803924       TRUE
105             10      20804721    20808310       20806515       TRUE
106             10      20808317    20808848       20808517       TRUE
107             10      20808855    20810907       20809888       TRUE
108             10      20811250    20814707       20813114       TRUE
109             10      20814714    20814861       20814774       TRUE
    fragmentLength leftFragEndLength rightFragEndLength leftFragEndValid
104           1548               229                260             TRUE
105           3589                19                 19            FALSE
106            531               102                232             TRUE
107           2052               136                121             TRUE
108           3457               547                276             TRUE
109            147                59                 85             TRUE
    rightFragEndValid leftFragEndReads rightFragEndReads fragEndReadsAverage
104              TRUE                2                 0                   1
105             FALSE                0                 0                   0
106              TRUE                1                 0                   0
107              TRUE                5                 0                   2
108              TRUE                0                 0                   0
109              TRUE                1                10                   6
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>