required_cols: Table of required columns

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

Table of required columns

Description

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
)

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.
embed_links	For any columns that contain URLs, embed them as links with shortened names.
verbose	Print messages.

Source

embedding knitr links

Examples

d <- required_cols(add_versions=TRUE, add_executables=TRUE)

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.