ntfreq

Description

Calculates nucleotide frequency of reads in bam file

Usage

ntfreq(bam_file, ntlength, toRNA = TRUE, count_type = "total")

Arguments

Value

Returns a data.frame of the frequency of nucleotides (either A/C/G/T or A/C/G/U) at each position up to the specified ntlength

Author(s)

Diana H.P. Low

Examples

data(ssviz)
freq<-ntfreq(pctrlbam,ntlength=10)

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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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(ssviz)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: reshape

Attaching package: 'reshape'

The following objects are masked from 'package:S4Vectors':

    expand, rename

Loading required package: ggplot2
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ssviz/ntfreq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ntfreq
> ### Title: ntfreq
> ### Aliases: ntfreq
> 
> ### ** Examples
> 
> data(ssviz)
> freq<-ntfreq(pctrlbam,ntlength=10)
No counts column provided in bam file. Running unique counts.
Otherwise provide a count matrix or run getCountMatrix.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>