linkage_phenotypes: Calculate linkage around SNP of interest and obtain...

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

Calculate linkage around SNP of interest and obtain phenotypes from phenotype table.

Description

Calculate linkage around SNP of interest and obtain phenotypes from phenotype table.

Usage

linkage_phenotypes(
  phenotype_table,
  phenotype,
  chrom,
  pos,
  nuc_range,
  ld_stats = "LLR",
  ld_cutoff = 10,
  SNPmatrix = "~/SNPmatrix.fst",
  specific = c("bx", "dag"),
  impacts = c("MODERATE", "HIGH")
)

Arguments

phenotype_table	A table containing phenotypes that should be retrieved. Column with accession IDs has to be name 'ACC_ID'
phenotype	Name of the phenotype of interest
chrom	Chromosome where the SNP of interest is
pos	Position of the SNP of interest on the chromosome
nuc_range	Range of nucleotides that will be analyzed (total, split evenly up and downstream of the SNP)
ld_stats	The LD statistics, see SNPStats::ld. Default is LLR
ld_cutoff	Only SNPs that have an LD values >= this will be plotted (default 10)
SNPmatrix	default "~/SNPmatrix.fst". If Needs to provided as a path to an fst file. Will be used for linkage calculation instead of polymorph. To use polymorph set to NULL
specific	(optional) treatment column that was used to split samples for specific GWAS.
impacts	SNP impacts to subset for can ("MODIFIER","LOW","MODERATE","HIGH"; default: c("MODERATE","HIGH"))

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.

For all SNPs that pass some criteria (see params), the phenotypes are then retrieved and split by presence of each SNP (SNP = TRUE or FALSE).

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