shazam (version 0.1.2)

collapseByClone: Identifies clonal consensus sequences

Description

Identifies effective/consensus sequences collapsed by clone

Usage

collapseByClone(db, cloneColumn = "CLONE", sequenceColumn = "SEQUENCE_IMGT", germlineColumn = "GERMLINE_IMGT_D_MASK", expandedDb = FALSE, regionDefinition = NULL, nonTerminalOnly = FALSE, nproc = 1)

Arguments

db

data.frame containing sequence data.

cloneColumn

character name of the column containing clonal identifiers.

sequenceColumn

character name of the column containing input sequences.

germlineColumn

character name of the column containing germline sequences.

expandedDb

logical indicating whether or not to return the expanded db, containing all the sequences (as opposed to returning just one sequence per clone collapsed by )

regionDefinition

RegionDefinition object defining the regions and boundaries of the Ig sequences.

nonTerminalOnly

logical indicating whether to include mutations at the leaves.

nproc

Number of cores to distribute the operation over. If the cluster has already been set earlier, then pass the cluster. This will ensure that it is not reset.

Value

A modified db data.frame with clonal consensus sequences in the CLONAL_SEQUENCE column.

Details

collapseByClone identifies the consensus sequence of each clonal group and appends a column to the input data.frame containing the clonal consensus for each sequence.

For sequences identified to be part of the same clone, this function defines an effective sequence that will be representative for all mutations in the clone. Each position in this consensus (or effective) sequence is created by a weighted sampling of each mutated base (and non "N", "." or "-" characters) from all the sequences in the clone.

For example, in a clone with 5 sequences that have a C at position 1, and 5 sequences with a T at this same position, the consensus sequence will have a C 50% and T 50% of the time it is called.

The function returns an updated db that collpases all the sequences by clones defined in the cloneColumn column argument.

Non-terminal branch mutations are defined as the set of mutations that occur on branches of the lineage tree that are not connected to a leaf. For computational efficiency, the set of non-terminal branch mutations is approximated as those that are shared between more than one sequence in a clone. In this case the terminal branch mutations are filtered out.

This function can be parallelized if db contains thousands of sequences. Specify the number of cores available using the nproc parameter.

See Also

See IMGT_SCHEMES for a set of predefined RegionDefinition objects.

Examples

# Subset example data
db <- subset(InfluenzaDb, CPRIMER %in% c("IGHA","IGHM") & 
                          BARCODE %in% c("RL016","RL018","RL019","RL021"))

# Run collapseByClone
db_new <- collapseByClone(db, cloneColumn="CLONE", 
                          sequenceColumn="SEQUENCE_IMGT",
                          germlineColumn="GERMLINE_IMGT_D_MASK",
                          expandedDb=FALSE,
                          regionDefinition=IMGT_V_NO_CDR3,
                          nproc=1)