correlationMethSNPs {MEAL} | R Documentation

## Computes the correlation between methylation and SNPs

### 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

    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:

- cpg: Name of the cpg

- exprs: Name of the expression probe

- beta: coefficient of the methylation change

- se: standard error of the beta

- P.Value: p-value of the beta coefficient

- adj.P.Val: q-value computed using B&H

[Package MEAL version 1.10.1 Index]