formatClones {dowser} | R Documentation |
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.
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,
...
)
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 |
majoronly |
only return largest subclone and sequences without light chains |
columns |
additional data columns to include in output |
... |
additional arguments to pass to makeAirrClone |
This function is a wrapper for makeAirrClone. Also removes whitespace, ;, :, and = from ids
A tibble of airrClone objects containing modified clones.
Executes in order makeAirrClone. Returns a tibble of airrClone objects which serve as input to getTrees and findSwitches.
data(ExampleAirr)
# Select two clones, for demonstration purpose
sel <- c("3170", "3184")
clones <- formatClones(ExampleAirr[ExampleAirr$clone_id %in% sel,],trait="sample_id")