assocComp-methods: Associate principal components with sample annotations
In qizhengyang2017/methylKit_1.8.1: DNA methylation analysis from high-throughput bisulfite sequencing results
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function associates principal components with sample annotations
such as age, gender, batch_id. Can be used to detect which batch effects
are associated with the variation in the methylation values.
Usage
1
assocComp(mBase, sampleAnnotation)
Arguments
mBase
methylBase or methylBaseDB
object with no NA values in the data part.
sampleAnnotation
a data frame where columns are different
annotations and
rows are the samples, in the same order as
in the methylBase object.
Value
a named list of principal component matrix (named 'pcs'),
by principal compopents (named 'vars') and a p-value matrix
showing association
p-values between sample annotations and principal components
(named 'association').
Author(s)
Altuna Akalin
Examples
1
2
3
data(methylKit)
sampleAnnotation=data.frame(batch_id=c("a","a","b","b"),age=c(19,34,23,40))
as=assocComp(mBase=methylBase.obj,sampleAnnotation)
qizhengyang2017/methylKit_1.8.1 documentation built on May 5, 2019, 7:58 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
This function associates principal components with sample annotations such as age, gender, batch_id. Can be used to detect which batch effects are associated with the variation in the methylation values.
Usage
1 | assocComp(mBase, sampleAnnotation)
|
Arguments
mBase |
|
sampleAnnotation |
a data frame where columns are different annotations and rows are the samples, in the same order as in the methylBase object. |
Value
a named list of principal component matrix (named 'pcs'), by principal compopents (named 'vars') and a p-value matrix showing association p-values between sample annotations and principal components (named 'association').
Author(s)
Altuna Akalin
Examples
1 2 3 | data(methylKit)
sampleAnnotation=data.frame(batch_id=c("a","a","b","b"),age=c(19,34,23,40))
as=assocComp(mBase=methylBase.obj,sampleAnnotation)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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