ewaff.sites | R Documentation |
Fit generalized linear model (GLM) to methylation levels each CpG site.
ewaff.sites(
formula,
variable.of.interest,
methylation,
data,
family = gaussian,
method = "glm",
generate.confounders = NULL,
n.confounders = NULL,
most.variable = NULL,
random.subset = 0.05,
...,
debug = F
)
formula |
An object of class |
variable.of.interest |
Name of variable(s) in the model formula
for which to save summary statistics. If it is the dependent variable
in the formula, then it must be numeric or binary; otherwise, it may
be any type of variable or even a vector of variables.
The value is ignored if |
methylation |
DNA methylation matrix, one row per CpG site, one column per sample. |
data |
Data frame of variables to include in the model. |
family |
See description for |
method |
Method for regressions: "glm", "rlm", "limma" or "coxph" (Default: "glm"). |
generate.confounders |
Generate variables from the methylation data
to adjust for unknown confounders. May be |
n.confounders |
Number of unknown confounders to generate. A value of
|
most.variable |
Generate confounders from the #' given most variable CpG sites rather than the whole matrix (Default: NULL). |
random.subset |
Generate surrogate variables from the given percentage of randomly selected CpG sites rather than the whole matrix (Default: 0.05, i.e. 5 percent). |
... |
Arguments to |
Note: mclapply
is used to fit regression models
using multiple cores.
List containing a table of association statistics ('table') and the model design matrix ('design').
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