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Releases: umr1283/dgapaq
Releases · umr1283/dgapaq
dgapaq 0.6.1
Minor improvements and fixes
- In rmarkdown templates,
- Fix wrong formula for heterozygosity outliers.
dgapaq 0.6.0
New feature
- In
R/convert_assembly.R
,convert_assembly()
allows to convert VCFs to target genome assembly
using the software CrossMap.
dgapaq 0.5.2
- In rmarkdown templates,
- Small refactoring.
- Ensure FID and IID are of type character.
dgapaq 0.5.1
- In rmarkdown templates,
- Fix wrong scale in homozygosity figure.
- Fix typos in homozygosity figure.
- Fix exclusion list in Excel.
dgapaq 0.5.0
- In
DESCRIPTION
,- Use
Suggests
instead ofImports
.
- Use
- In
R/qc_plink.R
,- Remove imports.
- In
R/qc_vcf.R
,- Remove imports.
dgapaq 0.4.1
- In rmarkdown templates,
- Reorder code in setup chunk.
dgapaq 0.4.0
Major improvements
-
- Now uses
data.table
. - Now uses
gt
. - Now uses
ggplot2
. - Improved text, figures and tables.
- Now uses
-
In
R/qc_vcf.R
andR/qc_plink.R
,- Core update based on new rmarkdown templates.
dgapaq 0.3.0
Minor improvements and fixes
- In rmarkdown template,
- Improve performance and memory consumption.
- In
R/qc_vcf.R
,- Update imports based on rmarkdown template.
dgapaq 0.2.0
Minor improvements and fixes
- In
DESCRIPTION
,- Remove dependendy to libterm-readkey-perl.
- Update all packages listed in
Imports
. - Now imports
ggplot2 v3.3.0
. - Now imports
gt
.
- Add the no read key version of HRC perl script.
- In rmarkdown template,
- Reorder YAML header in
qc_vcf()
. - Fix condition when be files are not available.
- Fix merge of files after check against reference panel.
- Fix combined vcf files not created.
- Fix issue with reference allele.
- Fix a typos in the names of a parameters.
- Fix gender check text printed when check was disabled.
- Fix condition when fasta file is not provided.
- Ensure missing values are moved before computing mean.
- Ensure scale for shape has always the right number of values.
- Add missing new line in summary.
- Add condition when no fasta file is provided.
- Reorder YAML header in
- In
R/qc_vcf.R
,- Add filenames and URLs to download needed files.
- In
R/qc_plink.R
,- Fix a typos in the names of a parameters.
- Now also work on non-binary PLINK files (i.e.,
.map
and.ped
).
dgapaq 0.1.10
Minor improvements and fixes
- In rmarkdown template, fix a typos in the names of a parameters.
- In
R/qc_plink.R
, fix a typos in the names of a parameters. - In
DESCRIPTION
, remove dependendy to libterm-readkey-perl.