co_methylation_step1: The first step of co-methylation analysis
In Gavin-Yinld/coMethy: Co-methylation analysis to cluster the genomic loci with similar methylation pattern
Description
Usage
Arguments
Value
Examples
View source: R/co_methylation_step1.R
Description
The first step of the co-methylation analysis, including kmeans analysis to group pCSM loci into three clusters, i.e. hypo/mid/hyper-methylation cluster, and, for each kmeans cluster, the network topology analysis function in WGCNA package is called to pick the soft-thresholding power.
Usage
1
co_methylation_step1(csm_ml_matrix)
Arguments
csm_ml_matrix
methylation profile of pCSM loci in each sample
Value
A list the following two components:
profile
the methylation profile of pCSM loci
modult_id
the label tells that which co-methylation module the pCSM loci belong to
Examples
1
2
3
4
library("coMethy")
file=paste(system.file(package="coMethy"),"extdata/co_methy.test.data.txt",sep='/')
meth_data <- read.table(file,sep='\t',header=T,row.names=1)
kmeans_cluster <- co_methylation_step1(meth_data)
Gavin-Yinld/coMethy documentation built on Aug. 23, 2019, 11:37 p.m.
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Description Usage Arguments Value Examples
View source: R/co_methylation_step1.R
Description
The first step of the co-methylation analysis, including kmeans analysis to group pCSM loci into three clusters, i.e. hypo/mid/hyper-methylation cluster, and, for each kmeans cluster, the network topology analysis function in WGCNA package is called to pick the soft-thresholding power.
Usage
1 | co_methylation_step1(csm_ml_matrix)
|
Arguments
csm_ml_matrix |
methylation profile of pCSM loci in each sample |
Value
A list the following two components:
profile |
the methylation profile of pCSM loci |
modult_id |
the label tells that which co-methylation module the pCSM loci belong to |
Examples
1 2 3 4 | library("coMethy")
file=paste(system.file(package="coMethy"),"extdata/co_methy.test.data.txt",sep='/')
meth_data <- read.table(file,sep='\t',header=T,row.names=1)
kmeans_cluster <- co_methylation_step1(meth_data)
|
R Package Documentation
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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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