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NEWS.md

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CARoT 0.10.0

Minor improvements and fixes

  • In DESCRIPTION,
    • Update rain to v0.5.1.
    • Update dmapaq to v0.3.4.
    • Remove NACHO.
    • Remove rain.
    • Remove other dependencies.

CARoT 0.9.0

  • In DESCRIPTION,
    • Update dgapaq to v0.6.0.

CARoT 0.8.2

  • In DESCRIPTION,
    • Update dgapaq to v0.5.2.
    • Update dmapaq to v0.3.3.

CARoT 0.8.1

  • In DESCRIPTION,
    • Update dmapaq to v0.3.2

CARoT 0.8.0

  • In DESCRIPTION,
    • Update dgapaq to v0.5.1.
    • Update dmapaq to v0.3.1.
    • Update rain to v0.5.0.

CARoT 0.7.0

Minor improvements and fixes

  • In DESCRIPTION,
    • Add back missing authors/contributors.
    • Update URLs with the new github repository.
    • Update packages version in Imports.
    • Update dgapaq to v0.2.0.
    • Update dmapaq to v0.2.0.
    • Update rain to v0.4.0.

CARoT 0.6.0

New features

  • Now attaches the R package dgapaq:
    • Remove R/qc_impute.R.
    • Remove R/qc_plinky.R.
    • Remove inst/perl/HRC-1000G-check.bim.pl.
  • Now attaches the R package dmapaq:
    • Remove R/qc_idats.R.
    • Remove R/read_idats.R.
    • Remove R/ggheatmap.R.
  • Remove the R package umr1283 from the list of attached packages.
  • Remove R/utils-pipe.R.
  • Remove R/utils-tidy-eval.R.

CARoT 0.5.0

New features

  • CARoT is now a meta-package:
    • Now attaches the R package umr1283.
    • Now attaches the R package MiSTr.
    • Now attaches the R package rain.
    • Now attaches the R package NACHO.
    • Now attaches the R package forcats.
    • Now attaches the R package stringr.
    • Now attaches the R package dplyr.
    • Now attaches the R package purrr.
    • Now attaches the R package readr.
    • Now attaches the R package tidyr.
    • Now attaches the R package tibble.
    • Now attaches the R package ggplot2.

Minor improvements and fixes

  • Remove R/mist.R, now attaches the R package MiSTr.
  • Remove R/estimate_ethnicity.R, now attaches the R package rain.
  • Use Rmarkdown template directory for qc_idats from umr1283.
  • Use Rmarkdown template directory for qc_impute from umr1283.
  • Use Rmarkdown template directory for qc_plink from umr1283.
  • In R/qc_idats.R,
    • add rgSet parameters to pass raw rgSet for normalisation and filtering.
    • now return raw rgSet and mSet.

CARoT 0.4.0

New features

  • New mist(), it allows to test for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statistics

Minor improvements and fixes

  • In R/pca_report.R,
    • rewrite core.
    • add check for overall outlier.
    • add example for roxygen.

CARoT 0.3.3

Minor improvements and fixes

  • In inst/rmarkdown/qc_idats.Rmd,
    • simplify some call to tidyverse functions.
    • add a parameter to control if PCA should be performed.
  • In R/qc_idats.R,
    • add a parameter to control if PCA should be performed.
  • In R/estimate_ethnicity.R,
    • include super pop and pop from 1K genome.

CARoT 0.3.2

Minor improvements and fixes

  • In inst/rmarkdown/qc_idats.Rmd,
    • fix and update "methods and parameters" section.
    • remove redundant code, i.e., as.data.frame.
    • suppress warnings for gender check, a plot is printed to allow diagnostic.
  • In R/estimate_ethnicity.R, complete roxygen documentation.

CARoT 0.3.1

Minor improvements and fixes

  • In inst/rmarkdown/qc_plink.Rmd,
    • in file-managementchunk, each plink steps to prepare files for imputation now generate different files to avoid names conflicts.
  • In R/qc_idats.R,
    • fix wrong annotation package for Illumina 450k methylation array.
    • change "MethPipe" with "CARoT" in messages.
  • In inst/rmarkdown/qc_idats.Rmd,
    • add cord blood panel for cell composition (only 450k).
    • merge methods and parameters sections.

CARoT 0.3.0

New features

  • New qc_impute(), it allows to compute post-imputation quality-control report using a default rmarkdown template (inst/rmarkdown/qc_impute.Rmd).

Minor improvements and fixes

  • In inst/rmarkdown/qc_plink.Rmd,
    • convert IID to character when reading files.
    • fix missing sheets in Excel exclusion file.
    • fix typos.
  • In R/estimate_ethnicity.R,
    • fix a wrong if statement when testing the parameters: input_type = "array" and splitted_by_chr = FALSE.
    • fix chromosome pattern recognition to allow VCF files to start with the chromosome id.
    • now check if binary exists at the path prodived in bin_path argument.
    • fix when IDs contains "_".
    • fix when chromosome id in VCF includes "chr".
    • add check_* functions.
    • export compute_pca().
    • add a vcf_half_call parameter to handle half-call when converting VCF to PLINK format.
  • In R/qc_plink.R,
    • fix roxygen doc for parameter n_cores to make it consistent with the current default values.
    • add cohort_name parameter.
  • In R/qc_idats.R,
    • change default parameter value for cohort_name.
    • fix roxygen doc for parameter n_cores to make it consistent with the current default values.
  • In inst/rmarkdown/qc_plink.Rmd,
    • replace signle quote with double quotes.
  • In R/pca_report.R, fix merge issue when the selected column was not "Sample_ID" (@mboissel, #2).

CARoT 0.2.1

Minor improvements and fixes

  • In inst/rmarkdown/qc_plink.Rmd,
    • fix YAML header with duplicated parameters.
    • fix duplicated chunk label.
    • fix cross-references.
    • fix variant call rate import.
    • tweak figures to make them more readable.
    • set include = FALSE for chunk without figure, table or text output.
    • add explicit na.rm = TRUE in geom_point() calls.
    • fix tidyr::separate() in relatedness_03 chunk by setting a more complex separator, i.e., "_-_".
    • replace underscore with dash in chunk names for cross-referencing.
    • fix column names in exclusion chunk.
    • make cross-cohort check only if multiple cohorts.
    • the studied population is now plotted in last in PCA.
    • add PCA plot with samples exclusion information.
    • multi-planes PCA plot now highlight outliers in all sub-plot.
    • decrease legend key size in PCA plots.
    • add a exclusion and flag summary in the last table.
    • fix typos.
  • In R/qc_plink.R,
    • fix params not declared in YAML header of inst/rmarkdown/qc_plink.Rmd.
    • complete roxygen documentation.
    • add start/end messages.
    • add prefix for messages.
  • In R/qc_idats.R,
    • add start/end messages.
    • add prefix for messages.
  • In R/pca_report.R,
    • fix a typo in roxygen documentation.
    • add start/end messages.
    • add prefix for messages.
  • In R/estimate_ethnicity.R,
    • add prefix for messages.

CARoT 0.2.0

New features

  • New qc_plink(), it allows to compute quality-control of genotyping array (PLINK format) using a default rmarkdown template (inst/rmarkdown/qc_plink.Rmd).

Minor improvements and fixes

  • In DESCRIPTION, add RSpectra (<= 0.13-1) for flashpcaR to Imports.
  • In DESCRIPTION, add data.table and qdap to Imports.

CARoT 0.1.7

Minor improvements and fixes

  • In inst/rmarkdown/qc_idats.Rmd, parameters are now described using question "should ... be removed?" instead of "remove ...".
  • In inst/rmarkdown/qc_idats.Rmd, now includes a section with the parameters used.
  • In R/qc_idats.R, fix a typo in the detection_pvalues parameter's documentation.

CARoT 0.1.6

Minor improvements and fixes

  • In R/estimate_ethnicity.R, add roxygen2 documentation for estimate_ethnicity().
  • In R/ggheatmap.R, add roxygen2 documentation for ggheatmap().
  • In R/pca_report.R, add roxygen2 documentation for pca_report().
  • In R/qc_idats.R, add roxygen2 documentation for qc_idats().
  • In man, add roxygen2 documentation for estimate_ethnicity(), ggheatmap(), pca_report() and qc_idats().

CARoT 0.1.5

Minor improvements and fixes

  • In inst/rmarkdown/qc_idats.Rmd, fix markdown typos.

CARoT 0.1.4

Minor improvements and fixes

  • In inst/rmarkdown/qc_idats.Rmd, fix Methods section describing what filter_ parameters do.

CARoT 0.1.3

Minor improvements and fixes

  • In R/qc_idats.R, decrease default dpi value from 300 to 120.
  • In inst/rmarkdown/qc_idats.Rmd, fix the bullet list in gender check section.

CARoT 0.1.2

Minor improvements and fixes

  • In R/estimate_ethnicity.R, add check_input() function to properly check inputs using fs package.
  • In inst/rmarkdown/qc_idats.Rmd, now print call rate parameters in plain text.
  • In inst/rmarkdown/qc_idats.Rmd and R/qc_idats.R, qc_idats() has a new cache parameter.

CARoT 0.1.1

Minor improvements and fixes

  • In format_sequencing() (R/estimate_ethnicity.R), fix missing arguments from format_vcf().
  • In inst/rmarkdown/qc_idats.Rmd, now applies filter_xy after gender check.
  • In inst/rmarkdown/qc_idats.Rmd, fix Sample_ID (i.e., rownames) for gender check.
  • In R/qc_idats.R, remove cat() messages from ENmix functions.

CARoT 0.1.0

New features

  • New read_idats(), it allows to efficiently import idats files mostly using minfi functions.
  • New estimate_ethnicity(), it allows to compute the genomic component for ethnicity based on VCF files.
  • New pca_report(), it allows to compute an analysis report using principal component analysis.
    The function can be used in Rmarkdown chunk with results="asis" to render the report.
  • New ggheatmap(), it allows to compute heatmap with dendrogram on x-axis and y-axis.
  • New qc_idats(), it allows to compute quality-control of methylation array from Illumina using a default rmarkdown template (inst/rmarkdown/qc_idats.Rmd).