summary_AclustsCCA: Outputs summary of AclustsCCA result

In jennyjyounglee/AclustsCCA: A Cluster Based Sparse Canonical Correlation Analayis to Test Associations Between A Multi-Pollutant Mixture and High-Dimentional DNA Methylation

Outputs summary of AclustsCCA result

Description

This function creates summary of AclustsCCA result table that summarizes A-clustering result.

Usage

summary_AclustsCCA(obj, annot, n.top = NULL)

Arguments

obj	Output of AclustsCCA
annot	A preloaded annotation file that includes columns the below name. For more information, IlluminaHumanMethylation450kanno.ilmn12.hg19. IlmnID: a character vector of IlmnID CHR: a numeric vector of chromosome containing the CpG Coordinate_37: a numeric vector of chromosomal coordinates of the CpG Islands_Name: a character vector of chromosomal coordinates of the CpG Island Relation_to_Island: a character vector of the location of the CpG relative to the CpG island UCSC_RefGene_Name: a character vector of Target gene name(s)
n.top	A number of top clusters with smallest p.value to show

Value

The function returns a table of summary characteristics for each cluster:

• ClustIdx: Index number of cluster corresponding to clusters.list

• CHR: a numeric value of chromosome containing the CpG

• UCSC_RefGene_Name: a list of target gene name(s)

• Islands_Name: a list of chromosomal coordinates of the CpG Island

• Significant: whether or not that cluster is significant

• Cancors: a numeric value of canonical correlation

• N.Probes: a number of probes in that cluster

• DMR.length: a length of DMR in base pairs

• Num.Exceed: a number of exceedness in permutation test

• Num.Perm: a number of permutation

• P.value: P.value corresponding to this cluster

• CpGs: CpG sites with non-zero loadings

• Exposures: Exposures with non-zero loadings

• CpGs.Loading: A loading vector of CpGs sites with non-zero loadings

• Exposures.Loading: A loading vector of exposures with non-zero loadings

jennyjyounglee/AclustsCCA documentation built on June 15, 2022, 7:45 p.m.