hypo_annotation_get loads the genome annotation.
hypo_annotation_get( searchLG, xrange, genes_of_interest = c(), genes_of_sec_interest = c(), anno_rown = 3 )
| searchLG | string scalar (mandatory), should be on of "LG01" - "LG24" |
|---|---|
| xrange | integer vector (mandatory), data range to be loaded(start bp - end bp). Positions are defined with respect to the LG, NOT the overall genomic position. |
| genes_of_interest | string vector (optional), tags specific gene names for highlighting when plotting. (needs to exactly match the gene name of the original gff file) |
| genes_of_sec_interest | string vector (optional), tags specific gene names for secondary highlighting when plotting. (needs to exactly match the gene name of the original gff file) |
| anno_rown | integer scalar (optional), defines the number of gene rows to avoid overlapping. |
Hypogen comes with the annotation data of the hamlet genome.
To load the data into R hypo_annotation_get makes use of
the rtracklayer package.
The function returns a list contain two data frames: the first one
holds the general mRNA extends, the second and the detailed Exon boundaries.
Only the data of a specified range on a specific LG is loaded. Genes of interest as well as genes of minor interest can be specified and the number of lines that the mRNAs can be specified to avoid overlapping when plotting the annotations.