check_required_cols: Check for necessary columns

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

Check for necessary columns

Description

Check whether the input data (dat) has the minimum columns required to run each fine-mapping method, as well as suggested columns.

Usage

check_required_cols(
  dat,
  finemap_methods = NULL,
  case_control = TRUE,
  verbose = TRUE
)

Arguments

dat	data.table containing SNP-level data to fine-map.
finemap_methods	Fine-mapping methods to run. See lfm for a list of all fine-mapping methods currently available.
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).
verbose	Print messages.

Examples

dat <- echodata::BST1
finemap_methods <- check_required_cols(dat=dat)

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