NEWS.md

dgapaq (development version)

dgapaq 0.7.0

New feature

• In R/compress_coverage.R,
  • compress_coverage() allows to compress coverage file (output of samtools depth) into contiguous segments based on position.
• In R/check_genotype.R,
  • create_genotype_matrix() allows to create a genotype matrix based on VCFs.
  • check_genotype() allows to check missing data in genotype matrix against coverage information.
• In R/tidy_vcf.R,
  • tidy_vcf() allows to correct missing genotypes in VCF using corrected genotype matrix (output of check_genotype())

Minor improvements and fixes

• In rmarkdown templates,
  • Fix number of duplicated samples in text.
  • Fix descriptive table, to not show duplicates.

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 of Imports.
• 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

• In rmarkdown templates,

  • Now uses data.table.
  • Now uses gt.
  • Now uses ggplot2.
  • Improved text, figures and tables.

• In R/qc_vcf.R and R/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.
• 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 0.1.0

New features

• qc_plink() allows to compute quality-control of genotyping array (PLINK format) using a rmarkdown template.
• qc_vcf() allows to compute post-imputation quality-control report using a default rmarkdown template.