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

araGenesA nicely formatted GRanges object
araGenomeThe araGenes object.
format_gwasRead an arbitrary GWAS table.
get_expressionGet expression data for a gene of interest
get_nearest_genesFind genes that are closest to a SNP.
get_overlapping_genesFind genes that overlap with a SNP.
get_phenotypeSubset a larger wide-format phenotype table to a defined...
get_polymorph_accQuery the 1001genomes API to obtain accession ids that carry...
intersect_expression_snpBased on a GeneID and a GWAS table and a rank, returns a...
intersect_phenotype_snpGet intersection between phenotype, and variant table.
plot_acc_mapPlot an interactive map of accessions that carry a SNP of...
plot_anchored_ldProduce a plot of linked SNPs
plot_annotated_gwasPlot annotated manhattan plot
plot_gwasBased on a GWAS table, generates a manhatten plot.
plot_intersect_expression_snpIntersect SNP presence with Gene expression.s
plot_intersect_phenotype_snpSplit phenotype table by SNP presence and plot
read_gwasRead a GWAS result file from limix (csv) and put it into a...
retrieve_countsBased on a GWAS table and a rank, returns a table of...
snp_linkageCalculate linkage around SNP of interest.
Gregor-Mendel-Institute/gwaR documentation built on Dec. 3, 2019, 4:52 p.m.