design: Create full and reduced design matrices for the cpg.assoc...
In CpGassoc: Association Between Methylation and a Phenotype of Interest

Description Usage Arguments Value Note Author(s) See Also Examples

Designed to be used by cpg.assoc and cpg.perm. Creates a full and reduced design matrices.

1	design(covariates, indep, chip.id, random)

`covariates`	A data frame consisting of the covariates of interest. covariates can also be a matrix if it is a model matrix minus the intercept column. It can also be a vector if there is only one covariate of interest. If no covariates must be specified as `NULL`.
`indep`	A vector containing the main variable of interest. `cpg.assoc` will evaluate the association between indep and the beta values.
`chip.id`	An optional vector containing chip or batch identities. If specified, `chip.id` will be included as a factor in the model.
`random`	Is the model going to be a mixed effects. If so, `chip.id` will not be included in the design matrices.

Returns a list containing the full and reduced design matrices.

`full`	The full design matrix.
`reduced`	The reduced design matrix.

The design function is designed to be used exclusively by the cpg.assoc and cpg.perm functions.

Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <rbarfield01@fas.harvard.edu>

cpg.assoc cpg.perm cpg.work plot.cpg scatterplot cpg.combine manhattan plot.cpg.perm

data(samplecpg,samplepheno,package="CpGassoc")
#Example where there are covariates:
covar<-data.frame(samplepheno$weight,samplepheno$Distance)
test<-design(covar,samplepheno$SBP,samplepheno$chip,FALSE)
dim(test$full)
dim(test$reduced)
test$reduced[1:5,1:5]
test$full[1:5,1:5]
#When no covariates or chip.id:
test2<-design(NULL,samplepheno$SBP,NULL,FALSE)
dim(test2$full)
dim(test2$reduced)

Loading required package: nlme
[1] 258  26
[1] 258  25
  (Intercept) samplepheno.weight samplepheno.Distance factor(chip.id)3
1           1           31.02998             28.49084                0
2           1           20.83885             13.10059                0
3           1           21.47078             14.76703                0
4           1           23.95091             25.54482                0
5           1           34.12922             29.45997                0
  factor(chip.id)4
1                0
2                0
3                0
4                0
5                0
  (Intercept)    indep samplepheno.weight samplepheno.Distance factor(chip.id)3
1           1 16.98629           31.02998             28.49084                0
2           1 34.90645           20.83885             13.10059                0
3           1 21.55838           21.47078             14.76703                0
4           1 20.90882           23.95091             25.54482                0
5           1 27.01004           34.12922             29.45997                0
[1] 258   2
[1] 258   1