bambu {bambu} | R Documentation

## long read isoform reconstruction and quantification

### Description

This function takes bam file of genomic alignments and performs isoform recontruction and gene and transcript expression quantification. It also allows saving of read class files of alignments, extending provided annotations, and quantification based on extended annotations. When multiple samples are provided, extended annotations will be combined across samples to allow comparison.

### Usage

    bambu(
        reads = NULL,
        rcFile = NULL,
        rcOutDir = NULL,
        annotations = NULL,
        genome = NULL,
        stranded = FALSE,
        ncore = 1,
        yieldSize = NULL,
        opt.discovery = NULL,
        opt.em = NULL,
        discovery = TRUE,
        verbose = FALSE
    )

### Arguments

`reads` | A string or a vector of strings specifying the paths of bam files for genomic alignments, or a `BamFile` object or a `BamFileList` object (see `Rsamtools`).
`rcFile` | A string or a vector of strings specifying the read class files that are saved during previous run of `bambu`.
`rcOutDir` | A string variable specifying the path to where read class files will be saved.
`annotations` | A `TxDb` object or A GRangesList object obtained by `prepareAnnotations`.
`genome` | A fasta file or a BSGenome object.
`stranded` | A boolean for strandedness, defaults to FALSE.
`ncore` | specifying number of cores used when parallel processing is used, defaults to 1.
`yieldSize` | see `Rsamtools`.
`opt.discovery` | A list of controlling parameters for isoform reconstruction process: prefix specifying prefix for new gene Ids (genePrefix.number), defaults to empty remove.subsetTx indicating whether filter to remove read classes which are a subset of known transcripts(), defaults to TRUE min.readCount specifying minimun read count to consider a read class valid in a sample, defaults to 2 min.readFractionByGene specifying minimum relative read count per gene, highly expressed genes will have many high read count low relative abundance transcripts that can be filtered, defaults to 0.05 min.sampleNumber specifying minimum sample number with minimum read count, defaults to 1 min.exonDistance specifying minum distance to known transcript to be considered valid as new, defaults to 35 min.exonOverlap specifying minimum number of bases shared with annotation to be assigned to the same gene id, defaults 10 base pairs
`opt.em` | A list of controlling parameters for quantification algorithm estimation process: maxiter specifying maximum number of run interations, defaults to 10000. bias specifying whether to correct for bias, defaults to FALSE. conv specifying the covergence trheshold control, defaults to 0.0001.
`discovery` | A logical variable indicating whether annotations are to be extended for quantification.
`verbose` | A logical variable indicating whether processing messages will be printed.

### Details

Main function

### Value

A list of two SummarizedExperiment object for transcript expression and gene expression.

### Examples

    ## =====================
    test.bam <- system.file("extdata",
        "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam",
        package = "bambu")
    fa.file <- system.file("extdata",
        "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa",
        package = "bambu")
    gr <- readRDS(system.file("extdata",
        "annotationGranges_txdbGrch38_91_chr9_1_1000000.rds",
        package = "bambu"))
    se <- bambu(reads = test.bam, annotations = gr,
        genome = fa.file,  discovery = FALSE)

[Package bambu version 1.2.1 Index]