set.genomic.region.subregion {Ravages} | R Documentation |
Variants annotation based on regions and subregions positions
Description
Attributes regions and subregions to variants based on given positions
Usage
set.genomic.region.subregion(x, regions, subregions, split = TRUE)
Arguments
x |
A bed.matrix |
regions |
A dataframe in bed format (start is 0-based and end is 1-based) containing the regions with the fields : |
subregions |
A dataframe containing the subregions in the same format as |
split |
Whether to split variants attributed to multiple regions by duplicating this variants, set at TRUE by default |
Details
Warnings: regions$Name
and subregions$Name
should be factors containing UNIQUE names of the regions, ORDERED in the genome order.
If x@snps$chr
is not a vector of integers, it should be a factor with same levels as regions$Chr
.
If a variant is attributed to multiple genomic regions, it will be duplicated in the bed matrix with one row per genomic region if split = TRUE
.
This function can be applied before using burden.subscores
to perform a functionally-informed burden tests with sub-scores for each SubRegion
within each genomic.region
.
Value
The same bed matrix as x with two additional columns: x@snps$genomic.region
containing the annotation of the regions
and x@snps$SubRegion
containing the annotation of the subregions
.
See Also
set.genomic.region
, burden.subscores
Examples
#Import 1000Genome data from region around LCT gene
x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)
#Group variants within known genes and
#Within coding and regulatory regions
x <- set.genomic.region.subregion(x,
regions = genes.b37, subregions = subregions.LCT)