MeripBamFileList-class {exomePeak2} | R Documentation

## Maintain and use BAM files in MeRIP-Seq experiment

### Description

An S4 object defined in exomePeak2 that summarizes the BAM files used in a MeRIP-Seq experiment.

`MeripBamFileList()` provide a convenient format to store and manage the BAM file directories for MeRIP-Seq data set.

This class contains BamFileList from the packge `Rsamtools`.

### Details

Constructors:

`MeripBamFileList` can be constructed by `scanMeripBAM()`

Accessors:

`MeripBamFileList` object share all the accessors with the BamFileList class, please check it for more information.

The frequently used accessors include:

`metadata()`: Return a list storing the design of MeRIP-Seq experiment.

`Parameter()`: Access to the BAM FLAG parameters used for BAM file filtering.

`asMate()`: Return a logical value, TRUE if the BAM file is paired end.

It has one additional accessor `LibraryType()`

`LibraryType()` retrieves the strand specificity information of the RNA-Seq library.

### Examples

    ### Define BAM File Directories

    f1 = system.file("extdata", "IP1.bam", package="exomePeak2")
    f2 = system.file("extdata", "IP2.bam", package="exomePeak2")
    f3 = system.file("extdata", "IP3.bam", package="exomePeak2")
    f4 = system.file("extdata", "IP4.bam", package="exomePeak2")
    IP_BAM = c(f1,f2,f3,f4)
    f1 = system.file("extdata", "Input1.bam", package="exomePeak2")
    f2 = system.file("extdata", "Input2.bam", package="exomePeak2")
    f3 = system.file("extdata", "Input3.bam", package="exomePeak2")
    INPUT_BAM = c(f1,f2,f3)

    f1 = system.file("extdata", "treated_IP1.bam", package="exomePeak2")
    TREATED_IP_BAM = c(f1)
    f1 = system.file("extdata", "treated_Input1.bam", package="exomePeak2")
    TREATED_INPUT_BAM = c(f1)

    ### For MeRIP-Seq Experiment Without the Treatment Group

    MeRIP_Seq_Alignment <- scanMeripBAM(
     bam_ip = IP_BAM,
     bam_input = INPUT_BAM,
     paired_end = FALSE
    )

    ### For MeRIP-Seq Experiment With the Treatment Group

    MeRIP_Seq_Alignment <- scanMeripBAM(
     bam_ip = IP_BAM,
     bam_input = INPUT_BAM,
     bam_treated_ip = TREATED_IP_BAM,
     bam_treated_input = TREATED_INPUT_BAM,
     paired_end = FALSE
    )

    LibraryType(MeRIP_Seq_Alignment)

    Parameter(MeRIP_Seq_Alignment)

[Package exomePeak2 version 0.99.98 Index]