Histogram of match length distribution of reads.

Description

Histogram of match length distribution of reads.

Usage

histMatchLength(aln, log10Transf = 0, titleHist)

Arguments

Value

A list with 2 elements. The first element: a data.frame of the number of counts per match length distribution. The second element in the list: a ggplot2 histogram of the match length distribution.

Examples

#starting from a GAlignment object
data(ctrlGAlignments)
aln <- ctrlGAlignments
#no log10 scaling
matchLenDistr <- histMatchLength(aln, 0)
#to plot the histogram
matchLenDistr[[2]]

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)

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> library(RiboProfiling)
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
Warning messages:
1: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling' 
2: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RiboProfiling/histMatchLength.Rd_%03d_medium.png", width=480, height=480)
> ### Name: histMatchLength
> ### Title: Histogram of match length distribution of reads.
> ### Aliases: histMatchLength
> 
> ### ** Examples
> 
> #starting from a GAlignment object
> data(ctrlGAlignments)
> aln <- ctrlGAlignments
> #no log10 scaling
> matchLenDistr <- histMatchLength(aln, 0)
> #to plot the histogram
> matchLenDistr[[2]]
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>