sequoia (version 2.4.1)

sequoia_report: Sequoia report

Description

Create a summary report of the genotype data and reconstructed pedigree, utilising a range of functions in the sequoia package. For many of the plots and tables, brief help on interpretation is provided.

Usage

sequoia_report(
  SeqList = NA,
  GenoM = NA,
  MaybeRel = NA,
  Conf = NA,
  comments = "",
  printcode = "yes",
  output_file = "",
  output_format = "html_document",
  copy_rmd = FALSE
)

Value

A file with the report in the specified output format.

Arguments

SeqList

list with output from sequoia. If not provided, all other input is ignored and an example report using the griffin data is generated.

GenoM

genotype matrix that was used to run sequoia.

MaybeRel

list with output from GetMaybeRel.

Conf

list with output from EstConf.

comments

optional comments to print at the top of the report.

printcode

include R code in the report ('yes', default) or not ('no'). The R code includes some brief notes and references to relevant functions.

output_file

filename (incl. path) for the report. Extension (.html, .pdf) not needed.

output_format

format for the report, e.g. 'html_document', rmarkdown::pdf_document(toc=TRUE, extra_dependencies = 'booktabs'), or bookdown::gitbook(split_by='none'). See render for details and options. Note that 'bookdown::gitbook', and possibly others, appear to only work after copying the .rmd file to the output folder.

copy_rmd

copy the .rmd file to the output folder? (i.e. same folder as output_file).

Details

The R markdown (.Rmd) file for the report is included with the package, and may freely be modified and re-used.

Examples

if (FALSE) {
sequoia_report(comments = 'This is a test',
               file = file.path(getwd(), 'test_griffins'))
}