The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
General:
New Features:
Added the function plotGenotypeConfidence, which
draws a genotype next to a color panel showing a per-gene confidence
value, such as the k_diff returned by
inferGenotypeBayesian.
Added the genotyped_alleles argument to
inferGenotypeBayesian. When TRUE, a
genotyped_alleles column is added with the most likely
alleles based on the highest Bayesian zygosity likelihood.
Added the allele_col argument to
plotGenotype to choose the column of alleles to plot (e.g.,
allele_col="genotyped_alleles").
Added the include_unseen and strip_d
arguments to genotypeFasta. With
include_unseen=TRUE, germline alleles of genes absent from
the genotype are also returned. genotypeFasta now uses the
genotyped_alleles column, when present, instead of
alleles.
Added the trim_seq, overwrite,
ignored_regex, treat_multigene_as_uncalled,
top_k, top_by, strip_d and
reassign_uncalled arguments to
reassignAlleles.
reassignAlleles now supports D and J calls. The
segment is determined from the prefix of the v_call
argument, and the result is written to the
v_call_genotyped, d_call_genotyped or
j_call_genotyped column accordingly. The
v_call column name must now begin with v,
d or j.
Backwards Incompatible Changes:
gene_cutoff is a fraction,
inferGenotype now computes the cutoff from the number of
sequences of the gene’s locus instead of the whole repertoire.
inferGenotype and inferGenotypeBayesian warn
when calls from more than one locus are detected.Bug Fixes:
reassignAlleles not realigning sequences when
only one sequence had a gene absent from the genotype.Performance:
reassignAlleles now uses
alakazam::seqMismatchMatrix and
alakazam::seqMismatchCount to compute Hamming distances,
and parses allele calls only once per unique call.Bug Fixes:
Updated plotNovel to display integer x-axis labels
in the mutation count plots.
Fixed findNovelAlleles to correctly dereference the
pos_range_max column name when filtering SNP
positions.
Documentation:
subsampleDb to use
set.seed for reproducibility.General:
tigger has moved to GitHub:
https://github.com/immcantation/tigger.Documentation:
General:
New Features:
pos_range_max argument to
findNovelAlleles and plotNovel. With
pos_range_max, TIgGER takes into account the position in
which the V sequence alignment ends based on the aligner (usually
pos_range_max="v_germline_end"). With
pos_range_max=NULL, mutation count uses all nucleotides in
the IMGT V region. This means that when the V is trimmed on the 3’,
TIgGER includes in the mutation count nucleotides from the CDR3.Bug Fixes:
Updated the error check in positionMutations to
check for both empty GERM_NT positions and absence of IMGT gaps in the
germline. Before, gapped germlines of less than 312 positions (
IGHV4-31*09, 311 positions) would have empty GERM_NT positions, and the
function would stop with an error message ‘Check you are using gapped
reference germlines’.
Fixed bug in selectNovel where
keep_alleles=T would not keep different alleles leading to
the same novel sequence.
Fixed bug genotypeFasta where it wouldn’t find
duplicate genes.
General:
Replaced error message with warning in function getMutatedAA, to allow for germlines with N (e.g. IGHV1-45*01)
To identify the closest reference, the
generateEvidence function will only consider reference
germlines belonging to the same gene segment. This is to avoid an error
when the user provides VDJ references, not just V.
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). 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.findNovelAlleles are now using lower case
(germline_call, not GERMLINE_CALL)General:
AIRRDb.Dependencies:
Bug Fixes:
sortAlleles that was not sorting correctly
TR gene names.positionMutations that was counting
. as mutated position.New Features:
GermlineIGHV and moved old annotations to
SampleGermlineIGHV.v_call), J call (j_call),
sequence alignment (seq), junction (junction)
and junction length (junction_length) in all functions that
use this information.reassignAlleles with
non-existent v_call column.generateEvidence that was reporting amino
acids mutations as NA instead of gaps.Bug Fixes:
reassignAlleles occurring with single
match genotypes.selectNovel improperly removing all identical
novel alleles, rather than keeping a single entry.genotypeFasta will now retain IMGT-numbering spacers as
. characters instead of converting them to -
characters.findNovelAlleles causing overly
aggressive minimum sequence threshold filtering.getPopularMutationCount.New Features:
inferGenotypeBayesian function.generateEvidence to build a complete
evidence table from the results of findNovelAlleles,
inferGenotype, inferGenotypeBayesian, and
reassignAlleles.findNovelAlleles and adjusted the definitions/names of some
existing columns.keep_gene argument of
reassignAlleles to provide options for maintaining
reassignments at the gene (previous TRUE behavior), family,
or repertoire level.findNovelAlleles.Backwards Incompatible Refactors:
germline_ighv,
sample_db, genotype and novel_df
to GermlineIGHV, SampleDb,
SampleGenotype and SampleNovel,
respectively.novel_df argument to novel in
selectNovel, inferGenotype, and
genotypeFasta.novel_df_row argument to
novel_row in plotNovel.inferGenotype was alter for
clarity.reassignAlleles so that
it returns the input data.frame with the V_CALL_GENOTYPED
column appended or overwritten.cleanSeqs will no longer replace .
characters with -.clip_db to data in
findNovelAlleles, plotNovel,
inferGenotype and reassignAlleles.findNovelAlleles.inferGenotype would break when
performing check for alleles that could not be distinguished.inferGenotype would break if all
sequences submitted were from a single gene and
find_unmutated was set to TRUE.findNovelAlleles() was not running
in parallel, even when nproc > 1.nproc=1 in
findNovelAlleles().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.