check_topSNPs: Check 'topSNPs'

In RajLabMSSM/echolocatoR: Automated genomic fine-mapping

Check topSNPs

Description

Check topSNPs. Creates a data.frame from the full summary stats if topSNPs is set to "auto".

Usage

check_topSNPs(topSNPs, fullSS_path, verbose = TRUE, ...)

Arguments

topSNPs	A data.frame with the genomic coordinates of the lead SNP for each locus. The lead SNP will be used as the center of the window when extracting subset from the full GWAS/QTL summary statistics file. Only one SNP per Locus should be included. At minimum, topSNPs should include the following columns: Locus A unique name for each locus. Often, loci are named after a relevant gene (e.g. LRRK2) or based on the name/coordinates of the lead SNP (e.g. locus_chr12_40734202) CHR The chromosome that the SNP is on. Can be "chr12" or "12" format. POS The genomic position of the SNP (in basepairs)
fullSS_path	Path to the full summary statistics file (GWAS or QTL) that you want to fine-map. It is usually best to provide the absolute path rather than the relative path.
verbose	Print messages.
...	Arguments passed on to echodata::import_topSNPs 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.

Value

data.frame

RajLabMSSM/echolocatoR documentation built on Jan. 29, 2023, 6:04 a.m.