applyFilters: Applies the specified set of filters to the data

In mbootwalla/MethylHose: Automated down stream processing of methylation data

Description

The function filters out the data for the probes that are specified by the user

Usage

applyFilters(x, filter = "all", custom.filter)

Arguments

x	A matrix containing beta values
filter	A character vector specifying the types of filters to apply. Can specify multiple filters.
custom.filter	A character vector containing the names of the probes to be filtered

Details

The function currently supports filtering of probes based only on the Illumina Methylation 450k platform. The following filters have been implemented:

none

No filtering is done

noncg

All non-CpG probes are filtered out. Non-CpG probes are probes that do not begin with ‘cg’

sex

All probes that are associated with the sex chromosomes are filtered out

snp

Probes that are associated with a common SNP (common SNP is a SNP with Minor Allele Frequency > 1% as defined by the UCSC snp135common track) within 10bp of the interrogated CpG site are filtered out

rpt

Probes that have 15bp from the interrogated CpG site overlapping with a known Repeat (as defined by RepeatMasker and TandemRepeatFinder) are filtered out

all

All the filters are applied to the data i.e. noncg, sex, snp and rpt

custom

This option is provided so that the user can apply their own customized filter instead of using the filters provided with the package. A character vector containing the names of the probes to be filtered out is expected

The script used to create the standard filters that have been provided with the package and can be found in ‘inst/scripts/createFilters.R’

Value

A matrix of filtered beta values

Author(s)

Moiz Bootwalla

mbootwalla/MethylHose documentation built on May 22, 2019, 12:57 p.m.