AbSeqRep-class: S4 class - AbSeqRepertoire analysis object

In malhamdoosh/abseqR: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

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)

malhamdoosh/abseqR documentation built on May 24, 2019, 12:36 a.m.