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

sampleBamFiles-class {rbamtools} | R Documentation

## Class `"sampleBamFiles"`: Data on multiple BAM files from an experimental setting.

### 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

[Package rbamtools version 2.16.17 Index]