Co-Expression Analysis of Sequencing Data


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Documentation for package ‘coseq’ version 1.24.0

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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