sampleBamFiles-class: Class '"sampleBamFiles"': Data on multiple BAM files from an...

In rbamtools: Read and Write BAM (Binary Alignment) Files

Description

The object contains data on location of BAM files, experimental group assignment and number of aligns per BAM file. The align-numbers are used for normalisation when alignment depth is plotted for single genes.

Objects from the Class

Objects can be created by calls of the form bs<-sampleBamFiles(object) where object is a numeric vector of length1.

Slots

bamFiles:

"character": Location of BAM files

bamIdxFiles:

"character": Location of BAM index files

nAligns:

"numeric": Total number of alignments in each BAM file.

group:

"factor": Group assignment

label

"character": Short textual identifier for each sample.

length

"integer": Vector length for bamFiles, bamIdxFiles, nAligns, group and label.

ev

"environment": Contains additional data (e.g. group table).

Methods

show

signature(object="sampleBamFiles"): Prints a short message with some summarizing data.

bamFiles

signature(object="sampleBamFiles": Returns names of BAM files.

bamIdxFiles

signature(object="sampleBamFiles"): Returns names of BAM index files.

length

signature(object="sampleBamFiles"): Returns number of BAM files.

nAligns

signature(object="sampleBamFiles"): Returns total number of aligns in BAM files.

sampleLabels

signature(object="sampleBamFiles"): Returns sample labels for BAM files.

sampleGroups

signature(object="sampleBamFiles"): Returns group assignment for BAM files.

groupTable

signature(object="sampleBamFiles"): Returns group table (if present).

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
bs <- sampleBamFiles(bam)
sampleLabels(bs) <- "s1"
sampleGroups(bs) <- "g1"
checkBamFiles(bs)
nAligns(bs) <- bamCountAll(bs)
bs

Example output

Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
[checkBamFiles] File check ok
[checkBamFiles] 1  BAM Files OK.
[checkBamFiles] 1  RefData   OK.
[checkBamFiles] BAM + RefData content OK.
[checkBamFiles] Check OK.
An object of class "sampleBamFiles"
Number of Files : 1 
Groups          : g1 
Group table:
g1 
 1 

rbamtools documentation built on Nov. 11, 2019, 5:09 p.m.