ConvertToPE_BAM {MACPET} | R Documentation

## Convert two BAM files into one paired-end BAM file.

### Description

Stage 2 in `MACPETUlt` needs a paired-end BAM file to run. This can be created in Stage 1 using the usable_1 and usable_2 fastq files created in Stage 0. However the user might have two single-end BAM files already created but not paired (by filtering with another way than that in Stage 0 or mapping using another algorithm than that in Stage 1) and only needs to run Stages 2 and 3 in `MACPETUlt`. `ConvertToPE_BAM` can be used on the two BAM files for pairing them, and the resulted paired-end BAM file can then be used in Stage 2 in `MACPETUlt`.

### Usage

    ConvertToPE_BAM(S1_AnalysisDir = "", SA_prefix = "MACPET",
      S1_BAMStream = 2e+06, S1_image = TRUE, S1_genome = "hg19",
      BAM_file_1 = "", BAM_file_2 = "", S1_makeSam = FALSE)

### Arguments

`S1_AnalysisDir` | The directory where the resulted paired-end BAM file will be saved.
`SA_prefix` | see `MACPETUlt`.
`S1_BAMStream` | see `MACPETUlt`.
`S1_image` | see `MACPETUlt`.
`S1_genome` | see `MACPETUlt`.
`BAM_file_1` | The directory of the BAM file with the first reads. Their Qnames have to end with /1.
`BAM_file_2` | The directory of the BAM file with the second reads. Their Qnames have to end with /2.
`S1_makeSam` | see `MACPETUlt`.

### Details

The BAM files `BAM_file_1` and `BAM_file_2` do not need to be sorted, but their Qnames have to end with /1 and /2 respectively. Furthermore, the BAM files have to include the header section.

### Value

A paired-end BAM file named `SA_prefix_MACPET_Paired_end.bam` and its index, saved in `S1_AnalysisDir`.

### Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

### References

Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.

### See Also

`MACPETUlt`, `SampleChIAPETDataRead_1.bam`, `SampleChIAPETDataRead_2.bam`

### Examples

    requireNamespace('ggplot2')

    #Create a temporary forder, or anywhere you want:
    S1_AnalysisDir=file.path(tempdir(),'MACPETtest')
    dir.create(S1_AnalysisDir)#where you will save the results

    #directories of the BAM files:
    BAM_file_1=system.file('extdata', 'SampleChIAPETDataRead_1.bam', package = 'MACPET')
    BAM_file_2=system.file('extdata', 'SampleChIAPETDataRead_2.bam', package = 'MACPET')
    SA_prefix='MACPET'

    #convert to paired-end BAM:
    ConvertToPE_BAM(S1_AnalysisDir=S1_AnalysisDir,
                    SA_prefix=SA_prefix,
                    S1_BAMStream=2000000,
                    S1_image=TRUE,
                    S1_genome='hg19',
                    BAM_file_1=BAM_file_1,
                    BAM_file_2=BAM_file_2)

    #test if the resulted BAM is paired-end:
    PairedBAM=file.path(S1_AnalysisDir,paste(SA_prefix,'_Paired_end.bam',sep=''))
    Rsamtools::testPairedEndBam(file = PairedBAM, index = PairedBAM)

    bamfile = Rsamtools::BamFile(file = PairedBAM,asMates = TRUE)
    GenomicAlignments::readGAlignmentPairs(file = bamfile,use.names = FALSE,
                                           with.which_label = FALSE,
                                           strandMode = 1)

    #-----delete test directory:
    unlink(S1_AnalysisDir,recursive=TRUE)

[Package MACPET version 1.0.0 Index]