Utilities returning the paths to BAM files untreated1_chr4.bam and untreated3_chr4.bam

Description

BAM file untreated1_chr4.bam contains the subset of untreated1.bam (single-end reads, "Pasilla" experiment) where only alignments located on chr4 (Fly) were kept.

BAM file untreated3_chr4.bam contains the subset of untreated3.bam (paired-end reads, "Pasilla" experiment) where only alignments located on chr4 (Fly) were kept.

FASTA file dm3_chr4.fa contains the full sequence of the D. melanogaster chromosome 4.

untreated1_chr4, untreated3_chr4 and chr4 return the path to those files.

Usage

untreated1_chr4()
untreated3_chr4()
dm3_chr4()

Details

See the pasilla data package for details about the "Pasilla" experiment (RNA-seq, Fly).

BAM files untreated1.bam and untreated3.bam contain single-end and paired-end reads aligned to reference genome BDGP Release 5 (aka the dm3 genome on the UCSC Genome Browser).

Fasta file dm3_chr4.fa from UCSC, the Apr. 2006 assembly of the D. melanogaster genome (dm3, BDGP Release 5): DNA sequence for fly chromosome 4.

Examples

untreated1_chr4()
untreated3_chr4()
dm3_chr4()

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(pasillaBamSubset)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pasillaBamSubset/pasillaBamSubset-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pasillaBamSubset-package
> ### Title: Utilities returning the paths to BAM files untreated1_chr4.bam
> ###   and untreated3_chr4.bam
> ### Aliases: pasillaBamSubset-package pasillaBamSubset untreated1_chr4
> ###   untreated3_chr4 dm3_chr4
> ### Keywords: utilities
> 
> ### ** Examples
> 
> untreated1_chr4()
[1] "/home/ddbj/local/lib64/R/library/pasillaBamSubset/extdata/untreated1_chr4.bam"
> untreated3_chr4()
[1] "/home/ddbj/local/lib64/R/library/pasillaBamSubset/extdata/untreated3_chr4.bam"
> dm3_chr4()
[1] "/home/ddbj/local/lib64/R/library/pasillaBamSubset/extdata/dm3_chr4.fa"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>