samplecpg

samplepheno

annotation

<dl>
 <dt>samplecpg</dt>
<dd>Matrix containing sample (fake) methylation data for 258 individuals over 1228 CpG sites</dd> <dt>samplepheno</dt>
<dd>Matrix with phenotype info for the 258 individuals</dd> <dt>annotation</dt>
<dd>Matrix with annotation information for the 1228 CpG sites</dd> 
</dl>

datasets

Sample Data CpGassoc

Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

R Barfield

CpGassoc

Association Between Methylation and a Phenotype of Interest

Sample Data CpGassoc function

<dl>
 <dt>samplecpg</dt>
<dd>Matrix, dimensions 1228 x 258</dd> <dt>samplepheno</dt>
<dd>Matrix, dimensions 258 x 6. Phenotype info on <code>"Dose"</code>, <code>"SBP"</code>, <code>"Distance"</code>, <code>"weight"</code>, <code>"Disease"</code>, and <code>"chip"</code></dd> <dt>annotation</dt>
<dd>Matrix, dimensions 1228 x 3. Header names are <code>"TargetID"</code>, <code>"CHR"</code>, and <code>"MAPINFO"</code></dd> 
</dl>

Format

<dl>
 <dt>samplecpg</dt>
<dd>Matrix containing sample (fake) methylation data for 258 individuals over 1228 CpG sites</dd>

 <dt>samplepheno</dt>
<dd>Matrix with phenotype info for the 258 individuals</dd>

 <dt>annotation</dt>
<dd>Matrix with annotation information for the 1228 CpG sites</dd>

 
</dl>

Sample data from CpGassoc — Sample Data CpGassoc

<dl>
 <dt>samplecpg</dt>
<dd>Matrix, dimensions 1228 x 258</dd>

 <dt>samplepheno</dt>
<dd>Matrix, dimensions 258 x 6. Phenotype info on <code>"Dose"</code>, <code>"SBP"</code>, <code>"Distance"</code>, <code>"weight"</code>, <code>"Disease"</code>, and <code>"chip"</code></dd>

 <dt>annotation</dt>
<dd>Matrix, dimensions 1228 x 3. Header names are <code>"TargetID"</code>, <code>"CHR"</code>, and <code>"MAPINFO"</code></dd>

 
</dl>

Sample Data CpGassoc: Sample data from CpGassoc

Description

Usage

Arguments

Format

See Also

Examples