add_variants | R Documentation |
Use this function to add variant annotations to your CESAnalysis by specifying variants to add in one of five ways: a data.table containing genomic coordinates (output from select_variants(), typically), a GRanges object, a BED file, another CESAnalysis, or SNV/AAC IDs.
add_variants(
target_cesa = NULL,
variant_table = NULL,
snv_id = NULL,
aac_id = NULL,
bed = NULL,
gr = NULL,
source_cesa = NULL,
padding = 0
)
target_cesa |
CESAnalysis to receive variant annotations |
variant_table |
A data.table with chr/start/end positions (1-based closed
coordinates, like MAF format). All possible SNVs overlapping the table's genomic
coordinates (within |
snv_id |
Character vector of CES-style SNV IDs to add. |
aac_id |
Character vector of AAC IDs (or short names, like "KRAS_G12C") |
bed |
A path to a BED file. All possible SNVs overlapping BED intervals (within
|
gr |
A GRanges object. All possible SNVs overlapping the ranges (within |
source_cesa |
Another CESAnalysis from which to copy snv_ids. SNVs will be re-annotated using the target_cesa's associated reference data. |
padding |
How many bases (default 0) to expand start and end of each gr range |
All methods of adding variants work by identifying which SNVs to add and then using the target_cesa's associated reference data to identify overlapping amino-acid-change mutations, which are then added as well. (You can't add just SNVs or just AACs.) Note that if you try to add far more distinct variants than appear in a typical cohort (as in, millions), annotation will take a while and the annotation tables in the CESAnalysis may take up significant memory. Please contact us if you have issues.
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