Documentation:
General:
locus
column to the package's example data, to satisfy
alakazam >= 1.3.0 requirements.Bug fixes:
Fixed a bug defineClonesScoper
where the bulk clonal clustering was using
light chain sequences. Now, light chain sequences are removed based on the
locus
information. If the column locus
does not exist, it is created with
alakazam::getLocus(v_call)
.
Fixed a bug in defineClonesScoper
where the split_light
part of the
algorithm was reanalyzing heavy chain v_calls and using this information to
sometimes split clone_id groups into subgroups. Only light chain v_calls
should be used for this. The bug could be observed in situations where
first=FALSE
and the 'linker' ambiguous heavy chain v_calls were left out of
the same clone_id group because of the junction distance threshold.
Fixed parallelization setup for defineClonesScoper
.
General:
General:
N
to any
characters except [ATCG]
.Cloning:
fields
argument to identicalClones
, hierarchicalClones
and
spectralClones
to allow for data partitioning prior to clonal assignment.cell_id
column.identicalClones
, hierarchicalClones
and
spectralClones
when specifying nproc
> 1.Backwards Incompatible Changes:
V_CALL
(Change-O) as the default to identify the field that stored
the V gene calls, they now use v_call
(AIRR). That means, scripts that
relied on default values (previously, v_call="V_CALL"
), will now fail if
calls to the functions are not updated to reflect the correct value for the
data. If data are in the Change-O format, the current default value
v_call="v_call"
will fail to identify the column with the V gene calls
as the column v_call
doesn't exist. In this case, v_call="V_CALL"
needs
to be specified in the function call.ExampleDb
converted to the AIRR Rearrangement standard and examples updated
accordingly.defineClonesScoper
function to three functions: identicalClones
,
hierarchicalClones
, and spectralClones
.General:
Cloning:
Deprecated:
analyzeClones
is deprecated. The clonal analysis has been added
to the main function defineClonesScoper
as an argument analyze_clones
.analyze_clones
set to be true, otherwise a single dataframe is
returned.plot_neighborhoods
from clonal analysis has been deprecated.neighborhoods
from clonal analysis has been deprecated.General:
hierarchical
for hierarchical-clustering based, and identical
for clustering among identical junction sequences are added.vj
in argument method
.Clonal analysis:
calculateInterVsIntra
function. Now, "inter" is the label used to form
distances that mean between clones, and "intra" is the label used to form
distances that mean on the inside, within each clone.plotInterVsIntra
output from a density plot to a histogram.Initial public release.