formatClones - Generate an ordered list of airrClone objects for lineage construction
Description¶
formatClones
takes a data.frame
or tibble
with AIRR or
Change-O style columns as input and masks gap positions, masks ragged ends,
removes duplicates sequences, and merges annotations associated with duplicate
sequences. If specified, it will un-merge duplicate sequences with different
values specified in the trait
option. It returns a list of airrClone
objects ordered by number of sequences which serve as input for lineage reconstruction.
Usage¶
formatClones(
data,
seq = "sequence_alignment",
clone = "clone_id",
subclone = "subclone_id",
nproc = 1,
chain = "H",
heavy = "IGH",
cell = "cell_id",
locus = "locus",
minseq = 2,
split_light = FALSE,
majoronly = FALSE,
columns = NULL,
...
)
Arguments¶
- data
- data.frame containing the AIRR or Change-O data for a clone. See makeAirrClone for required columns and their defaults
- seq
- sequence alignment column name.
- clone
- name of the column containing the identifier for the clone. All entries in this column should be identical.
- subclone
- name of the column containing the identifier for the subclone.
- nproc
- number of cores to parallelize formating over.
- chain
- if HL, include light chain information if available.
- heavy
- name of heavy chain locus (default = “IGH”)
- cell
- name of the column containing cell assignment information
- locus
- name of the column containing locus information
- minseq
- minimum numbner of sequences per clone
- split_light
- split or lump subclones? See
getSubclones
. - majoronly
- only return largest subclone and sequences without light chains
- columns
- additional data columns to include in output
- …
- additional arguments to pass to makeAirrClone
Value¶
A tibble of airrClone objects containing modified clones.
Details¶
This function is a wrapper for makeAirrClone. Also removes whitespace, ;, :, and = from ids
Examples¶
data(ExampleAirr)
# Select two clones, for demonstration purpose
sel <- c("3170", "3184")
clones <- formatClones(ExampleAirr[ExampleAirr$clone_id %in% sel,],trait="sample_id")
See also¶
Executes in order makeAirrClone. Returns a tibble of airrClone objects which serve as input to getTrees and findSwitches.