polymorph_impact: Retrieve impacts of SNPs within a certain range around a GWAS...

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

Retrieve impacts of SNPs within a certain range around a GWAS peak. Uses snpmatrix for genotype lookup

Description

Retrieve impacts of SNPs within a certain range around a GWAS peak. Uses snpmatrix for genotype lookup

Usage

polymorph_impact(
  gwas_table,
  rank,
  nuc_range,
  SNPmatrix,
  use_phenotype_table = NULL,
  acc_col
)

Arguments

gwas_table	Object returned from format_gwas function
rank	The (-log10(p)) rank of the SNP of interest
nuc_range	Window around the SNP of interest to retrieve information for.
SNPmatrix	The path to the snpmatrix to use for identifying accessions that carry the relevant SNP.
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	the column that contains accession identifiers.

Details

Based on a Phenotype table, the name of the phenotype and a GWAS table and a rank, produces a boxplot of that phenotype, grouped by presence of that SNP.

See Also

get_phenotype

format_gwas

phenotype_by_snp

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