MeripBamFileList-class: Maintain and use BAM files in MeRIP-Seq experiment

In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

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)

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.