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Table of required columns

Source: R/required_cols.R
required_cols.Rd

Return a table with the minimum columns required to run each fine-mapping method, as well as suggested columns.

Usage

required_cols(
  case_control = TRUE,
  for_all = c("SNP", "CHR", "POS", "Effect", "StdErr"),
  add_versions = FALSE,
  add_sources = TRUE,
  add_citations = TRUE,
  add_executables = FALSE,
  embed_links = FALSE,
  verbose = TRUE
)

Source

embedding knitr links

Arguments

case_control

Whether the summary statistics come from a case-control study (e.g. a GWAS of having Alzheimer's Disease or not) (TRUE) or a quantitative study (e.g. a GWAS of height, or an eQTL) (FALSE).

for_all

Columns required for all methods.

add_versions

Add software versions for each method.

add_sources

Add source code URLs for each method.

add_citations

Add citations for each method.

add_executables

Add path to executables for each method.

For any columns that contain URLs, embed them as links with shortened names.

verbose

Print messages.

Examples

if (FALSE) { # \dontrun{
d <- required_cols(add_versions=TRUE, add_executables=TRUE)
} # }