AbSeqRep-class {abseqR} | R Documentation

## S4 class - AbSeqRepertoire analysis object

### Description

The AbSeqRep object contains all metadata associated with the AbSeq (python backend) run conducted on it. This S4 class represents a single sample(repertoire) and it can be "combined" with other samples by using the `+` operator to create an AbSeqCRep object. This value, in turn, can be used as the first argument to report which generates a comparison between all samples included in the `+` operation.

Users do not manually construct this class, but rather indirectly obtain this class object as a return value from the abseqReport and report functions.

### Value

AbSeqRep

### Slots

`f1`

  character. Path to FASTA/FASTQ file 1.

`f2`

  character. Path to FASTA/FASTQ file 2.

`chain`

  character. Type of chain, possible values:

  - hv

  - lv

  - kv

  - klv

  each representing Heavy, Lambda and Kappa respectively.

`task`

  character. Type of analysis conducted, possible values:

  - all

  - annotate

  - abundance

  - diversity

  - productivity

  - fastqc

  - primer

  - 5utr

  - rsasimple

  - seqlen

  - secretion

  - seqlenclass

`name`

  character. Name of analysis.

`bitscore`

  numeric. Part of filtering criteria: V gene bitscore filter value.

`qstart`

  numeric. Part of filtering criteria: V gene query start filter value.

`sstart`

  numeric. Part of filtering criteria: V gene subject start filter value.

`alignlen`

  numeric. Part of filtering criteria: V gene alignment length filter value.

`clonelimit`

  numeric. Number of clones to export into csv file. This is only relevant in `-t all` or `-t diversity` where clonotypes are exported into `<outdir>/<name>/diversity/clonotypes`

`detailedComposition`

  logical. Plots composition logo by IGHV families if set to true, otherwise, plots logos by FR/CDRs.

`log`

  character. Path to log file.

`merger`

  character. Merger used to merge paired-end reads.

`fmt`

  character. File format of `file1` and (if present) `file2`. Possible values are FASTA or FASTQ.

`sites`

  character. Path to restriction sites `txt` file. This option is only used if `-t rsasimple`

`primer5end`

  ANY. Path to 5' end primer FASTA file.

`primer3end`

  ANY. Path to 3' end primer FASTA file.

`trim5`

  numeric. Number of nucleotides to trimd at the 5' end;

`trim3`

  numeric. Number of nucleotides to trimd at the 3' end;

`outdir`

  character. Path to output directory

`primer5endoffset`

  numeric. Number of nucleotides to offset before aligning 5' end primers in `primer5end` FASTA file.

`threads`

  numeric. Number of threads to run.

`upstream`

  character. Index (range) of upstream nucleotides to analyze. This option is only used if `-t 5utr` or `-t secretion`.

`seqtype`

  character. Sequence type, possible values are either `dna` or `protein`.

`database`

  character. Path to IgBLAST database.

`actualqstart`

  numeric. Query sequence's starting index (indexing starts from 1). This value overrides the inferred query start position by AbSeq.

`fr4cut`

  logical. The end of FR4 is marked as the end of the sequence if set to TRUE, otherwise the end of the sequence is either the end of the read itself, or trimmed to `--trim3 <num>`.

`domainSystem`

  character. Domain system to use in IgBLAST, possible values are either `imgt` or `kabat`.

### See Also

`abseqReport` returns a `list` of `AbSeqRep` objects.

### Examples

    # this class is not directly constructed by users, but as a return
    # value from the abseqReport method.

    # Use example data from abseqR as abseqPy's output, substitute this
    # with your own abseqPy output directory
    abseqPyOutput <- tempdir()
    file.copy(system.file("extdata", "ex", package = "abseqR"), abseqPyOutput, recursive=TRUE)
    samples <- abseqReport(file.path(abseqPyOutput, "ex"), report = 0)

[Package abseqR version 1.0.0 Index]