convertToASC(): prepare data and germline for haplotype
inference using PIgLET Allele Similarity Clusters (ASC), resolving
duplicated genes and aligning with OGRDB reference sets.
Dependencies:
Reduced the dependency footprint: removed gtools,
RColorBrewer, dendextend, rlang
and methods; moved plotly,
htmlwidgets and ggdendro to Suggests (loaded
only when needed); moved ggplot2 to Imports.
General:
Replaced the deprecated ggplot2::aes_string()
usage.
Added a testthat test suite.
Migrated the repository to GitHub with continuous integration and an
online documentation site.
Version 0.3.0: Dec 9, 2024
General:
Minor bug fix to createHaplotypeTable for haplotyping using IGHD
genes.
Version 0.2.9: Oct 28, 2024
General:
Minor bug fix to createHaplotypeTable for IGH haplotypes
Version 0.2.8: July 29, 2024
General:
Minor bug fix to createHaplotypeTable for TRB haplotypes
Version 0.2.7: July 2, 2024
General:
Minor bug fix to createHaplotypeTable
Version 0.2.6: April 26, 2024
General:
Minor bug fix to hapDendo
Version 0.2.5: February 6,
2023
General:
Removed deprecated function of dplyr
Version 0.2.4: September 14,
2022
General:
Generalized the createFullHaplotype to allow other genes as
anchor.
Version 0.2.3: March 14, 2022
General:
Fixed a bug in the haplotype plot, cases where a gene is within the
haplotype table but not in the gene_order flag.
Version 0.2.1: February 16,
2022
General:
updated the package for changes in dependencies for the haplotype
plots.
add a new function readHaplotypeDb for reading
haplotype tables created from createFullHaplotype. For
tables downloaded from VDJbase.org, reading the files into R is
recommended with the new function.
Version 0.1.6: June 10, 2020
Backwards Incompatible Changes:
From this version the gene order within plots can be determined by
the genes_order variable. The variable receives a vector of the ordered
genes. If not supplied the default order for the genes is by the
GENE.loc order which can be found in the package using
data("GENE.loc").
Hereby, the gene_order variable has been removed.
General:
updated the package for TRB haplotypes.
Version 0.1.5: June 10, 2020
Backwards Incompatible Changes:
Changed default expected data format from the Change-O data format
to the AIRR Rearrangement standard. For example, where functions used
the column name 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, toHap_col=“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 toHap_col=“v_call” will fail to identify the column with the V
gene calls as the column v_call doesn’t exist. In this case,
toHap_col=“V_CALL” needs to be specified in the function call.
For consistency with the style of the new data format default, field
names in all other user exposed data structures have been updated to use
the same font case style.
General:
Updated dependencies to R >= 3.5.0, dplyr >= 1.0.0, ggplot2
>= 3.2.0, alakazam >= 1.0.0, tigger >= 1.0.0, and tidyr
>=1.0.0.
Version 0.1.4: January 28,
2020
Fixed bug within the hapHeatmap visualization.
Version 0.1.3.999: November
18, 2019
Adapted deletionsByVpooled to infer single chromosome
deletion from light chain repertoire.
Added html5 interactive output for deletionHeatmap
visualization.
Version 0.1.3: September 8,
2019
Optimized hapHeatmap visualization, r base graph.
Version 0.1.2: July 25, 2019
Improved visualization of short read sequences annotation.
Version 0.1.1: May 8, 2019
Improved createFullHaplotype run-time
Fixed a bug wherein createFullHaplotype miss-handled
novel allele labels
Version 0.1.0: March 4, 2019
Initial public release.
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