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NEWS.md

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analysis_templates (development version)

  • R/targets/

    • tar_crossmap.R, targets setup to upgrade or downgrade genome assembly of VCF files.
    • tar_ewas.R, targets setup to perform multiple EWAS.
    • tar_genotype.R, targets setup to compute PLINK files quality-control.
    • tar_gsea.R, targets setup to compute gene-set enrichment analysis.
    • tar_gwas.R, targets setup to perform multiple GWAS using PLINK2 software.
    • tar_methylation.R, targets setup to compute idats (methylation) files quality-control.
    • tar_ora.R, targets setup to compute over-representation analysis.
    • tar_vep.R, targets setup to compute VEP annotations.

  • R/functions/

    • tar-crossmap.R, functions, used in tar_crossmap.R, to upgrade or downgrade genome assembly of VCF files.
    • tar-ewas.R, function, used in tar_ewas.R, to perform multiple EWAS.
    • tar-gwas.R, function, used in tar_gwas.R, to perform multiple GWAS using PLINK2 software.
    • tar-manhattan.R, functions to draw Manhattan plot using ggplot2.
    • tar-plink2.Rn function to download PLINK2 binary.
    • tar-pval_trans.R, p-value ggplot2 axis transformation.
    • tar-qc_idats.R, functions, used in tar_methylation.R, to compute idats (methylation) files quality-control.
    • tar-qc_plink.R, functions, used in tar_genotype.R, to compute PLINK files quality-control.
    • tar-sub_chunk.R, function to create sub-chunk inside a chunk in RMarkdown.
    • tar-vep.R, functions, used in tar_vep.R, to prepare Docker command and to format VEP output.

  • R/rmarkdown/ (assets directory from github.com/umr1283/xaringan-template is required)

    • ewas_report.Rmd, xaringan report template associated with R/targets/tar_ewas.R and R/functions/tar-ewas.R.
    • genotype_array_qc_report.Rmd, xaringan report template associated with R/targets/tar_genotype.R and R/functions/tar-qc_plink.R.
    • gwas_report.Rmd, xaringan report template associated with R/targets/tar_gwas.R and R/functions/tar-gwas.R.
    • methylation_array_qc_report.Rmd, xaringan report template associated with R/targets/tar_methylation.R and R/functions/tar-qc_idats.R.

  • R/scripts

    • **-****.R,
      • fix project name to not include file extension.
      • trim trailing spaces.
    • default.R,
      • default R script.
    • 01-design.R,
      • skeleton script make batch design for omics (currently "empty").
    • 02-qc_idats.Rmd,
      • YAML header for Rmarkdown template in umr1283/dmapaq.
    • 02-qc_idats_snps.Rmd,
      • YAML header for Rmarkdown template in umr1283/dmapaq (mostly for mQTL analysis).
    • 03-qc_plink.Rmd,
      • skeleton script or YAML header for Rmarkdown template in umr1283/dgapaq.
    • 04-qc_impute.Rmd,
      • skeleton script or YAML header for Rmarkdown template in umr1283/dgapaq.
    • 05-ethnicity.R,
      • skeleton script to perform ethnicity inference using 1,000 Genomes and HRC imputed VCF files.
    • 06-omni_to_hg38.R,
      • skeleton R script to upgrade genotyping arrays to GRCh38 genome assembly.
    • 07-save_outputs.R,
      • skeleton R script to store "sensitive"/"fragile" data to a more secure disk.
    • 08-vep_vcf_docker.R,
      • skeleton R script with iterative steps to retrieve RSID and gene's symbol using VEP (Docker).
      • add function to prepare docker command and to format output.
    • 09-gwas.R,
      • skeleton R script to perform a GWAS using PLINK2 with multiple traits.
    • 10-ewas.R,
      • skeleton R script to perform a EWAS using limma with multiple traits.
      • tweak & refactor some code.
      • use as.matrix from data.table.
    • 11-twas.R,
      • skeleton R script to perform a GWAS using DESeq2 with multiple traits.
      • fix #2 (@Ning-L).
      • ensure Ensembl ID does not contain version.
    • 12-ora.R,
      • add gene symbols for KEGG.
    • 13-gsea.R and R/tar_gsea.R,
      • add genes set and peripheral sets (genes set - core set).
      • add gene symbols in addition to Ensembl, Uniprot or Entrez gene IDs.
      • fix ties using pvalue as secondary parameter in sorting and removing .Machine$double.eps for the second value.
    • 14-mqtl.R,
      • skeleton R script to perform mQTL analysis (methylation Vs. genotypes).
      • fix missing variables.
      • tweak & refactor some code.
      • use as.matrix from data.table.
    • 15-eqtl.R,
      • keleton R script to perform eQTL analysis (expression Vs. genotypes).
      • fix missing variables.
    • 16-eqtm.R,
      • new expression-methylation analysis.
      • tweak & refactor some code.
      • isoform/transcript or gene level.
    • 16-eqtm_estimated_time.R, new script to estimate computation time from 16-eqtm.R's log.