correlationMethSNPs: Computes the correlation between methylation and SNPs

Description Usage Arguments Details Value

View source: R/correlationMethSNPs.R

Description

Estimates the correlation between methylation and expression. When there are known variables that affect methylation and/or expression, their effect can be substracted using a linear model and then the residuals are used.

Usage

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correlationMethSNPs(multiset, meth_set_name = NULL, snps_set_name = NULL,
  range, variable_names, covariable_names = NULL, snps_cutoff = 0.01,
  verbose = TRUE)

Arguments

multiset

MultiDataSet containing a methylation and an expression slots.

meth_set_name

Character vector with the name of the MultiDataSet's slot containing methylation data.

snps_set_name

Character vector with the name of the MultiDataSet's slot containing SNPs data.

range

GenomicRanges with the range used in the analñysis

variable_names

Character vector with the names of the variables that will be used to obtain the methylation residuals. By default, none is used and residuals are not computed.

covariable_names

Character vector with the names of the variables that will be used to adjust the model.

snps_cutoff

Numerical with the threshold to consider a p-value from a SNP-cpg correlation significant.

verbose

Logical value. If TRUE, it writes out some messages indicating progress. If FALSE nothing should be printed.

Details

For each cpg, a range is defined by the position of the cpg plus the flank parameter (upstream and downstream). Only those expression probes that are entirely in this range will be selected. For these reason, it is required that the ExpressionSet contains a featureData with the chromosome and the starting and ending positions of the probes.

Value

List with the results:


MEAL documentation built on May 24, 2018, 6:02 p.m.