ASEset from bam file

Description

count alleles and create an ASEset direct from bam file instead of reading into R first.

Usage

ASEsetFromBam(gr, ...)

## S4 method for signature 'GRanges'
ASEsetFromBam(gr, pathToDir, PE = TRUE,
  flagsMinusStrand = c(83, 163), flagsPlusStrand = c(99, 147),
  strandUnknown = FALSE, ...)

Arguments

Details

counts the alleles in a bam file based on GRanges positions.

Author(s)

Jesper R. Gadin

Examples

data(GRvariants)
gr <- GRvariants

##no execution at the moment
#pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance')
#a <- ASEsetFromBam(gr, pathToDir)
 

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 '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(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
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: GenomeInfoDb
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: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/ASEsetFromBam.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEsetFromBam
> ### Title: ASEset from bam file
> ### Aliases: ASEsetFromBam ASEsetFromBam,GRanges-method
> ### Keywords: ASEset
> 
> ### ** Examples
> 
> 
> data(GRvariants)
> gr <- GRvariants
> 
> ##no execution at the moment
> #pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance')
> #a <- ASEsetFromBam(gr, pathToDir)
>  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>