snp_linkage: Calculate linkage around SNP of interest.

In Gregor-Mendel-Institute/gwaR: A collection of R functions to conduct GWAS analysis (in Arabidopsis thaliana)

Calculate linkage around SNP of interest.

Description

Calculate linkage around SNP of interest.

Usage

snp_linkage(
  gwas_table,
  rank,
  anchored = FALSE,
  plot = FALSE,
  SNPmatrix = NULL,
  nuc_range = 50000,
  ld_depth = 1000,
  ld_stats = "LLR",
  ld_symmetric = FALSE,
  ld_cutoff = 10,
  ld_legend = FALSE,
  add_ld_band = FALSE,
  use_phenotype_table = NULL,
  acc_col = "ACC_ID",
  use_all_acc = FALSE,
  data_only = FALSE
)

Arguments

gwas_table	Object returned from format_gwas function
rank	Rank of the SNP of interest
anchored	Perform anchored analysis. If TRUE Linkage will only be estimated for the SNP of interest, and the surrounding ones, but not between surrounding SNPs.
plot	Default FALSE. Should a plot be returned, instead of the table? Only supported for anchored = T
SNPmatrix	default NULL. Needs to provided as a path to an fst file. Will be used instead of polymorph.
nuc_range	Range of nucleotides that will be analyzed (total, split evenly up and downstream of the SNP)
ld_depth	Maximum SNP distance to calculate LD for (only relevant when anchored = FALSE)
ld_stats	The LD statistics, see SNPStats::ld. Default is LLR
ld_symmetric	Should a symmetric matrix be returned? see SNPStats::ld
ld_cutoff	Only SNPs that have an LD values >= this will be plotted (default 10)
ld_legend	Toggle color legend for LD. Off by default.
add_ld_band	add a layer showing the LD as a lot of lines. (default FALSE)
use_phenotype_table	If supplied: Genotypes listed here will be used for linkage analysis. Otherwise, all accessions that carry this SNP will be included.
acc_col	Name of the column containing accession identifiers in the phenotype table
use_all_acc	If true, will override use_phenotype_table and use all 1135 sequenced accessions.
data_only	Return the data used for plotting, instead of the plot, defaults to FALSE.

Details

This function calculates LD in a specific region.

The SNPs per accession in the region are retrieved from polymorph or from a provided SNPmatrix.

Sometimes, the ld function produces no result, especially when used with anchored = T.

anchored analysis will use one SNP can compute LD of that SNP against a region.

Default settings return the LD table.

Gregor-Mendel-Institute/gwaR documentation built on Feb. 8, 2023, 8:34 p.m.