Co-Expression Analysis of Sequencing Data

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Documentation for package ‘coseq’ version 1.24.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

coseq-package	Co-expression and co-abundance analysis of high-throughput sequencing data
clusterEntropy	Calculation of per-cluster entropy
clusterInertia	Calculation of within-cluster inertia
clusters	Accessors for the assigned cluster labels of a coseqResults object.
clusters-method	Accessors for the assigned cluster labels of a coseqResults object.
compareARI	Pairwise comparisons of ARI values among a set of clustering partitions
compareARI-method	Pairwise comparisons of ARI values among a set of clustering partitions
compareARI-methods	Pairwise comparisons of ARI values among a set of clustering partitions
compareICL	Compare corrected ICL values after data transformation
convertLegacyCoseq	Convert legacy coseq objects
coseq	Co-expression or co-abudance analysis of high-throughput sequencing data
coseq-method	Co-expression or co-abudance analysis of high-throughput sequencing data
coseq-methods	Co-expression or co-abudance analysis of high-throughput sequencing data
coseqFullResults	Accessors for the assigned cluster labels of a coseqResults object.
coseqFullResults-method	Accessors for the assigned cluster labels of a coseqResults object.
coseqGlobalPlots	Visualize results from coseq clustering
coseqModelPlots	Visualize results from coseq clustering
coseqResults	coseqResults object and constructor
coseqResults-class	coseqResults object and constructor
coseqRun	Co-expression analysis
DDSEextract	Accessors for the assigned cluster labels of a coseqResults object.
DDSEextract-method	Accessors for the assigned cluster labels of a coseqResults object.
Djumpextract	Accessors for the assigned cluster labels of a coseqResults object.
Djumpextract-method	Accessors for the assigned cluster labels of a coseqResults object.
fietz	RNA-seq data from the mouse neocortex in Fietz et al. (2012)
ICL	Accessors for the assigned cluster labels of a coseqResults object.
ICL-method	Accessors for the assigned cluster labels of a coseqResults object.
kmeansProbaPost	Calculate conditional probabilities of cluster membership for K-means clustering
likelihood	Accessors for the assigned cluster labels of a coseqResults object.
likelihood-method	Accessors for the assigned cluster labels of a coseqResults object.
logclr	Calculate the Log Centered Log Ratio (logCLR) transformation
matchContTable	Permute columns of a contingency table
model	Accessors for the assigned cluster labels of a coseqResults object.
model-method	Accessors for the assigned cluster labels of a coseqResults object.
nbCluster	Accessors for the assigned cluster labels of a coseqResults object.
nbCluster-method	Accessors for the assigned cluster labels of a coseqResults object.
NormMixClus	Normal mixture model estimation and selection for a series of cluster numbers
NormMixClusK	Normal mixture model estimation
NormMixParam	Calculate the mean and covariance for a Normal mixture model
plot	Visualize results from coseq clustering
plot-method	Visualize results from coseq clustering
plot-methods	Visualize results from coseq clustering
proba	Accessors for the assigned cluster labels of a coseqResults object.
proba-method	Accessors for the assigned cluster labels of a coseqResults object.
profiles	Accessors for the assigned cluster labels of a coseqResults object.
profiles-method	Accessors for the assigned cluster labels of a coseqResults object.
show	Accessors for the assigned cluster labels of a coseqResults object.
show-method	Accessors for the assigned cluster labels of a coseqResults object.
summary	Summarize results from coseq clustering
summary-method	Summarize results from coseq clustering
summary-methods	Summarize results from coseq clustering
tcounts	Accessors for the assigned cluster labels of a coseqResults object.
tcounts-method	Accessors for the assigned cluster labels of a coseqResults object.
transformationType	Accessors for the assigned cluster labels of a coseqResults object.
transformationType-method	Accessors for the assigned cluster labels of a coseqResults object.
transformRNAseq	Transform RNA-seq data using common transformations