import_topSNPs: Import top GWAS/QTL summary statistics

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Import top GWAS/QTL summary statistics

Description

The resulting topSNPs data.frame can be used to guide the finemap_loci in querying and fine-mapping loci.

Usage

import_topSNPs(
  topSS,
  sheet = 1,
  startRow = 1,
  cols = NULL,
  munge = TRUE,
  colmap = construct_colmap(),
  min_POS = NULL,
  max_POS = NULL,
  grouping_vars = c("Locus"),
  remove_variants = NULL,
  show_table = FALSE,
  verbose = TRUE
)

Arguments

topSS	Can be a data.frame with the top summary stats per locus. Alternatively, you can provide a path to the stored top summary stats file. Can be in any tabular format (e.g. excel, .tsv, .csv, etc.). This file should have one lead GWAS/QTL hits per locus. If there is more than one SNP per locus, the one with the smallest p-value (then the largest effect size) is selected as the lead SNP. The lead SNP will be used as the center of the locus when constructing the locus subset files.
sheet	If the topSS file is an excel sheet, you can specify which tab to use. You can provide either a number to identify the tab by order, or a string to identify the tab by name.
startRow	first row to begin looking for data. Empty rows at the top of a file are always skipped, regardless of the value of startRow.
cols	A numeric vector specifying which columns in the Excel file to read. If NULL, all columns are read.
munge	Standardise column names.
colmap	Column mappings object. Uses construct_colmap by default.
min_POS	Column containing minimum genomic position (used instead of an arbitrary window size).
max_POS	Column containing maximum genomic position (used instead of an arbitrary window size).
grouping_vars	The variables that you want to group by such that each grouping_var combination has its own index SNP. For example, if you want one index SNP per QTL eGene - GWAS locus pair, you could supply: grouping_vars=c("Locus","Gene").
remove_variants	SNPs to remove from topSS,
show_table	Create an interative data table.
verbose	Print messages.
Locus	Column containing unique locus name.

Value

Munged topSNPs table.

Examples

topSNPs <- echodata::import_topSNPs(
    topSS = echodata::topSNPs_Nalls2019_raw,
    colmap = construct_colmap(P = "P, all studies",
                              Effect = "Beta, all studies",
                              Locus = "Nearest Gene",
                              Gene = "QTL Nominated Gene (nearest QTL)"
                              ),
    grouping_vars = "Locus Number")

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.