Description Usage Arguments Details
Plots is a negative log base 10 p-value against genomic position scatterplot for a relatively small genomic "window". Below this Association layer, there are additional layers or "tracks" providing biological context: hg19 build 37 combined Recombination Rate, known refSeq Genes, and optional tracks including genetic regulation information.
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data |
A genetic association results dataframe. |
recomb_map |
A recombination map dataframe with header and
obligatory columns 'position' (genomic position), 'combined_rate'
(combined recombination rate cM/Mb), and 'chr' (chromosome). Use
|
target |
A character vector for the variant of interest. |
chromosome |
An integer indicating the chromosome on which the region sits. |
target_bp |
A integer indicating base pair position in the centre of the region. |
pop |
A string argument passed to LDlinkR. A 1000 Genomes population codes, or super population codes can be used. Multiple codes allowed. Default is super population "EUR" (includes "CEU", "TSI", "FIN", "GBR", "IBS"). |
window_kb |
A integer indicating window size in kb (default is
150kb), to be included either side of the |
regulation |
A boolean (default |
token |
An LDlinkR 'Personal Access Token'. Default is 'NULL'. See Details. |
You will need a genetic map. Use get_map
to download 1000 Genomes phase 3 recombination map data. To retrieve LD data for the region of interest, you will need an LDlinkR 'Personal Access Token' described here. Apply for a token here.
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