| remove_snps {methrix} | R Documentation |
Removes CpG sites from the object if they overlap with common SNPs
remove_snps(m, populations = NULL, maf_threshold = 0.01, reduce_filtering = FALSE, forced = FALSE)
m |
|
populations |
Populations to use. Default is all. |
maf_threshold |
The frequency threshold, above which the SNPs will be removed. Accepted thresholds: 0.01 and 0.05. Default is 0.05 |
reduce_filtering |
If TRUE, the SNPs with a MAF < 0.1 will be evaluated and only the highly variable ones will be removed. Default FALSE. |
forced |
the reduce_filtering is not recommended with less than 10 samples, but can be forced. Default is FALSE. |
Takes methrix object and removes common SNPs. SNPs overlapping with a CpG site and have a minor allele frequency (MAF)
above a threshold in any of the populations used will be selected and the corresponding CpG sites will be removed from the methrix object.
With the reduce_filtering option, SNPs with MAP < 0.1 will be further evaluated. If they show low variance in the dataset, there is probably no genotype
variability in the population, therefore the corresponding CpG site won't be removed. Please keep in mind that variance thresholds are
a coverage or methylation matrix
data('methrix_data')
remove_snps(m = methrix_data, maf_threshold=0.01)