Man pages for Gregor-Mendel-Institute/gwaR
A collection of R functions to conduct GWAS analysis (in Arabidopsis thaliana)
| araGenes | araGenome as a nicely formatted GRanges object |
| araGenome | The araGenome object. |
| expression_by_snp | Based on a GWAS table and a rank, returns a table of... |
| format_gwas | Read an arbitrary GWAS table. |
| get_accessions | Obtain accession ids that carry a SNP. This function takes a... |
| get_expression | Get expression data for a gene of interest |
| get_nearest_genes | Find genes that are closest to a SNP. |
| get_overlapping_genes | Find genes that overlap with a SNP. |
| get_phenotype | Subset a larger wide-format phenotype table to a defined... |
| limix500rows | limix example output; 500 random rows |
| linkage_phenotypes | Calculate linkage around SNP of interest and obtain... |
| mine_gene | Get information from thalemine. |
| phenotype_by_snp | Get intersection between phenotype, and SNP presence. |
| plot_acc_map | Plot an interactive map of accessions that carry a SNP of... |
| plot_gwas | Plot annotated manhattan plot |
| polymorph_impact | Retrieve impacts of SNPs within a certain range around a GWAS... |
| read_limix | Read a GWAS result file from limix (csv) and put it into a... |
| sequenced_accessions | A list of sequenced accessions as of 2020 |
| snp_linkage | Calculate linkage around SNP of interest. |
