remove_snps: Removes CpG sites from the object if they overlap with common...

In CompEpigen/methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

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,
  n_chunks = 1,
  n_cores = 1
)

Arguments

m	methrix object
populations	Populations to use. Default is all.
maf_threshold	The frequency threshold, above which the SNPs will be removed. Default is 0.01
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.
n_chunks	Number of chunks to split the methrix object in case it is very large. Can only be used if input data is in HDF5 format. Default = 1.
n_cores	Number of parallel instances. Can only be used if input data is in HDF5 format. n_cores should be less than or equal to n_chunks. If n_chunks is not specified, then n_chunks is initialized to be equal to n_cores. Default = 1.

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)

CompEpigen/methrix documentation built on Sept. 23, 2023, 7:14 p.m.