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. |
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