expression_by_snp: Based on a GWAS table and a rank, returns a table of...

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

Based on a GWAS table and a rank, returns a table of expression values for a gene where accessions that contain the SNP have TRUE in SNP. If no GeneID is specified, the gene that is closest to the SNP will be looked up.

Description

Based on a GWAS table and a rank, returns a table of expression values for a gene where accessions that contain the SNP have TRUE in SNP. If no GeneID is specified, the gene that is closest to the SNP will be looked up.

Usage

expression_by_snp(
  gwas_table,
  SNPrank,
  GeneID = NULL,
  plot = FALSE,
  nobees = FALSE,
  SNPmatrix = NULL,
  ...
)

Arguments

gwas_table	Object returned from format_gwas function
SNPrank	The (-log10(p)) rank of the SNP of interest
GeneID	If NULL (default), retrieves counts for the gene that is nearest. If not NULL it should be a TAIR GeneID ("ATXGNNNNN"). If a GeneID is provided expression of that gene will be intersected with the SNP presence.
plot	If TRUE, will return a plot instead of a table.
nobees	If TRUE, observations will be plotted with geom_point.
SNPmatrix	SNPmatrix, to control if accessions are based on 1001genomes.org or local matrix.

See Also

format_gwas

get_expression

get_nearest_genes

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