remove_snps {methrix}R Documentation

Removes CpG sites from the object if they overlap with common SNPs

Description

Removes CpG sites from the object if they overlap with common SNPs

Usage

remove_snps(
  m,
  populations = NULL,
  maf_threshold = 0.01,
  reduce_filtering = FALSE,
  forced = FALSE,
  keep = FALSE
)

Arguments

m

methrix object

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.

keep

Do you want to keep the sites that were filtered out? In this case, the function will return with a list of wo methrix objects.

Details

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

Value

methrix object or a list of methrix objects

Examples

data('methrix_data')
remove_snps(m = methrix_data, maf_threshold=0.01)

[Package methrix version 1.0.05 Index]