AlignmentsExperimentSet-class {amplican} | R Documentation

## An S4 class to represent alignments from multiple experiments

### Description

Class `AlignmentsExperimentSet` holds data from multiple alignments for many experiments. Allows to examine alignments in great detail.

### Usage

    AlignmentsExperimentSet(...)

    ## S4 method for signature 'AlignmentsExperimentSet'
    length(x)

    ## S4 method for signature 'AlignmentsExperimentSet'
    fwdReads(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    fwdReads(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    rveReads(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    rveReads(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    fwdReadsType(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    fwdReadsType(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    rveReadsType(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    rveReadsType(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    unassignedData(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    unassignedData(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    readCounts(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    readCounts(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    experimentData(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    experimentData(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    barcodeData(x)

    ## S4 replacement method for signature 'AlignmentsExperimentSet'
    barcodeData(x) <- value

    ## S4 method for signature 'AlignmentsExperimentSet'
    unassignedCount(x)

    ## S4 method for signature 'AlignmentsExperimentSet'
    assignedCount(x)

    ## S4 method for signature 'AlignmentsExperimentSet'
    names(x)

    ## S4 method for signature 'AlignmentsExperimentSet'
    c(x, ...)

    ## S4 method for signature 'AlignmentsExperimentSet,numeric,missing,missing'
    x[i, j, ...,
      drop = TRUE]

    ## S3 method for class 'AlignmentsExperimentSet'
    as.list(x, ...)

    ## S4 method for signature 'AlignmentsExperimentSet'
    x$name

    ## S4 method for signature 'AlignmentsExperimentSet'
    writeAlignments(x, file = "",
      aln_format = "txt")

    ## S4 method for signature 'AlignmentsExperimentSet'
    lookupAlignment(x, ID, read_id = 1)

    ## S4 method for signature 'AlignmentsExperimentSet'
    extractEvents(object,
      use_parallel = FALSE)

### Arguments

`...` | pass any number of AlignmentsExperimentSet objects, make sure experiment IDs can be unique after merging
`x, object` | (AlignmentsExperimentSet)
`value` | Represents assignment values for setter methods.
`i, j, name, drop` | (numeric, missing, character, missing) AlignmentsExperimentSet object can be subsetted using names of the experiments eg. `x$name` or `x[i]`, resulting in AlignmentsExperimentSet object that has only one experiment. During this subsetting, values of unassignedData and barcodeData are dropped.
`file` | (connection or string) Destination file. When empty, defaults to standard output.
`aln_format` | ("txt" or "fasta") Specifies format of the file.
`ID` | (string) Experiment Identifier
`read_id` | (numeric) Read Identifier. Reads are sorted by frequency. Defaults to 1, most abundant read.
`use_parallel` | (boolean) When using `extractEvents` you can use multicore back-end through `register` as this is very slow function (despite vectorization).

### Value

depending on the function used

### Slots

`fwdReads,rveReads`

  (list) Named list where each element is of class `PairwiseAlignmentsSingleSubject`. Names correspond to the experiment ID. Contains alignments of reads against amplicons.

`fwdReadsType,rveReadsType`

  (list) Named list where each element is of logical vector, so far TRUE corresponds to HDR events. Names correspond to the experiment ID. Contains type of read - HDR/NHEJ.

`readCounts`

  (list) Named list where each element is numeric vector that describes how many reads are compressed into unique representation before alignment in `fwdReads` and/or `rveReads`.

`unassignedData`

  (data.frame) Contains reads that failed to be assigned to any of the experiments. Alignment of forward against reverse reads may give hint whether these reads are compromised in any way.

`experimentData`

  (data.frame) Expands on configuration file and provides information about cut rates, frameshifts, PRIMER DIMER detection etc. Each row corresponds to experiment ID.

`barcodeData`

  (data.frame) Information that is gathered on the barcode level is gathered in this data.frame, mainly quality filtering statistics.

### View alignments

Write out all alignments in "fasta" or "txt" format.:
`writeAlignments(x, file = "", aln_format = "txt")`

Write out human readable alignments for given experiment and read_id.:
`lookupAlignment(x, ID, read_id = 1)`

### Coercion based on events

Coerce to `data.frame` compatible with `GRanges` .:
as.data.frame(x)

### Examples

    exampleAlignments <- Biostrings::pairwiseAlignment(
      Biostrings::DNAStringSet(c("ACTGACTG", "CGACGACG")), "ACGTACGTACGT")
    new("AlignmentsExperimentSet",
         fwdReads = list(ID_1 = exampleAlignments, ID_2 = exampleAlignments),
         rveReads = list(ID_1 = exampleAlignments, ID_2 = exampleAlignments),
         fwdReadsType = list(ID_1 = c(FALSE, FALSE), ID_2 = c(FALSE, FALSE)),
         rveReadsType = list(ID_1 = c(FALSE, FALSE), ID_2 = c(FALSE, FALSE)),
         readCounts = list(ID_1 = c(2, 20), ID_2 = c(30, 100)),
         unassignedData = NULL,
         experimentData = data.frame(ID = c("ID_1", "ID_2"),
                                     Barcode = c("B1", "B1"),
                                     whatever = c(50, 100)),
         barcodeData = data.frame(Barcode = "B1", statistic1 = 100))
    # Coercion
    extractEvents(AlignmentsExperimentSet())
    GenomicRanges::GRanges(extractEvents(AlignmentsExperimentSet()))

[Package amplican version 1.8.2 Index]