NumericAnalysis: Correlation Analysis for each numeric covariate.

In JoshuaTian/EpiCluster: Clustering of (epigenetic) DNA methylation data using a variational Bayes NMF algorithm

Description

This function provide analysis that correlates the K inferred basis components, each a vector of length equal to the number of samples, to numeric factors. These factors could represent numeric phenotypes or batch only (e.g. age). User could use this function to detect if estimated componetes have effect on each numeric covariates. Apart from that, this function also provide enrichment analysis between clusters from RPBMM and each covariate, for this analysis we will use Krustal Test for numeric covariates.

Usage

NumericAnalysis(Basis,clusters,covariant,threshold,maxlevel,
                cov.name="This")

Arguments

Basis	Basis matrix from bgNMF function, which contain information of each estimated components.
clusters	clusters detected by EpiCluster function, shall be gathered already by maxlevel value in EpiAnalysis function.
covariant	A vector of numeric value, indicating one covariate of these samples, for example age.
threshold	After EpiCluster function, RPBMM may return clusters will different contained samples (even after combination with maxlevel parameter above), if there is only very little samples in one cluster, it may be pointless to do analysis(Krustal or Chisquare Test) between this cluster and various covariates. Thus user may set minimum threshold here to filter clusters contain numbers of samples less than this threshold. The default threshold is 10, which means, the function will automatically ignore all clusters(even after combination of maxlelve parameter above) contain numbers of sample less than 10.
maxlevel	Parameter control levels of RPBMM trees node will be analysis. After EpiCluster method, maybe too many branchs of trees will be generated, so we may need to assemble some of them by higher branch node, which is decided by users' research. The maxlevel parameter determine the maxium levels of binary trees will be specified. The default value for maxlevel is NULL, which means all branchs will be considered as a cluster, which might result to too many clusters. Thus, users should assign a proper maxlevel according to their aim.
cov.name	name for this covariate. If not specificed, it will be assigned as "This".

Details

Normally this function will not be used by user. It will be employed inside EpiAnalysis function automatically.

Value

Totally, there are five returned value, but for numeric covariates, only first four value will be assigned, the last one will be omitted.

cor.spearman	Correlation Analysis Result with Spearman method for each component (latent variables).
cor.pearson	Correlation Analysis Result with Pearson Correlation method for each component (latent variables).
Krustal	Krustal Test result conducted between filtered clusters and numeric covariates.
AOV	ANOVA Test result conducted between filtered clusters and numeric covariates.
ChisquareTest	Chisquare Test applied between filtered clusters and categorical covariates. It will be set NULL here.

Author(s)

Yuan Tian, Zhanyu Ma, Andrew Teschendorff

References

Yuan T, Ma Z, Beck S, Teschendorff AE. (2015). A fast variational Bayes dimensional reduction and clustering algorithm for Epigenome-Wide Association Studies (EWAS). Under Review.

Examples

    DataSet <- GenSimData(Ncpg=1000,Npheno=4,Nsig=100)
    EpiCluster.Result <- EpiCluster(DataSet$beta,nIter=20)
    EpiAnalysis.Result <- EpiAnalysis(EpiCluster.Result,
                                      PhenoTypes=DataSet$pheno.v,
                                      maxlevel=3,
                                      threshold=10)

JoshuaTian/EpiCluster documentation built on May 20, 2019, 10:19 p.m.