MeripBamFileList-class {exomePeak2} | R Documentation |
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
.
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.
### 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)