Compute post-imputation quality-control report using a default rmarkdown template.

qc_impute(input_directory = NULL, output_directory = NULL,
  cohort_name = "CARoT", output_file = paste0(cohort_name,
  "_imputation_QC.html"), title = "Post-Imputation Quality-Control",
  author_name = "CARoT", author_affiliation = NULL,
  author_email = NULL, cache = FALSE, show_code = FALSE,
  n_cores = 1, dpi = 120, gg_fontsize = 12, encoding = "UTF-8",
  ...)

Arguments

input_directory

A character. The path to the VCF files.

output_directory

A character. The path to the output directory.

cohort_name

A character. The name of the studied cohort / population.

output_file

A character. The name of the html file produced.

title

A character. The report's title. Default is "Post-Imputation Quality-Control".

author_name

A character. The author's name to be printed in the report. Default is CARoT.

author_affiliation

A character. The affiliation to be printed in the report. Default is NULL.

author_email

A character. The email to be printed in the report. Default is NULL.

cache

A logical. Should the R code be cached? Default is FALSE.

show_code

A logical. Should the R code be printed in the report? Default is FALSE.

n_cores

A numeric. The number of CPUs to use to estimate the ethnicity. Default is 1.

dpi

A numeric. The value for dpi when plotting the data. Default is 120.

gg_fontsize

A numeric. Value for the font size. Default is 12.

encoding

A character. The encoding to be used for the html report. Default is "UTF-8".

...

Parameters to pass to rmarkdown::render().