kableResults: Create association analysis results table in HTML or LaTeX

In Genentech/midasHLA: R package for immunogenomics data handling and association analysis

Create association analysis results table in HTML or LaTeX

Description

kableResults convert results table (runMiDAS output) to HTML or LaTeX format.

Usage

kableResults(
  results,
  colnames = NULL,
  header = "MiDAS analysis results",
  pvalue_cutoff = NULL,
  format = getOption("knitr.table.format"),
  scroll_box_height = "400px"
)

Arguments

results	Tibble as returned by runMiDAS.
colnames	Character vector of form c("new_name" = "old_name"), used to rename results colnames.
header	String specifying results table header.
pvalue_cutoff	Number specifying p-value cutoff for results to be included in output. If NULL no filtering is done.
format	String "latex" or "html".
scroll_box_height	A character string indicating the height of the table.

Value

Association analysis results table in HTML or LaTeX.

Examples

midas <- prepareMiDAS(hla_calls = MiDAS_tut_HLA,
                      colData = MiDAS_tut_pheno,
                      experiment = "hla_alleles")
object <- lm(disease ~ term, data = midas)
res <- runMiDAS(object, experiment = "hla_alleles", inheritance_model = "additive")
kableResults(results = res,
             colnames = c("HLA allele" = "allele"))

Genentech/midasHLA documentation built on Feb. 12, 2024, 9:38 a.m.