chroGPS2: Generation, visualization and differential analysis of epigenome maps

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Documentation for package ‘chroGPS’ version 2.0.1

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addVar Plot vector of a quantitative variable over a MDS map.
adjustPeaks Adjust peak width so that samples obtained under different conditions become comparable.
adjustPeaks-method Adjust peak width so that samples obtained under different conditions become comparable.
adjustPeaks-methods Adjust peak width so that samples obtained under different conditions become comparable.
as.matrix-method Class '"distGPS"'
bg3 Sample binding site and related data from BG3 cell line in Drosophila melanogaster.
bg3.tab Sample binding site and related data from BG3 cell line in Drosophila melanogaster.
bg3names Sample binding site and related data from BG3 cell line in Drosophila melanogaster.
boostMDS Improve goodness-of-fit of a given MDS solution in terms of R-square.
clusGPS Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusGPS-class Class '"clusGPS"'
clusGPS-method Class '"clusGPS"'
clusGPS-method Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusGPS-methods Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusNames Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusNames-method Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusterID Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
clusterID-method Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
combineGenesMatrix Combine two datasets with epigenetic factor profiles at gene level in order to produce a differential chroGPS-genes map.
contour2dDP Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
d Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
d.origs Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
d2 Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
d3 Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
diffFactors Performs differential analysis of chroGPS-factors maps based on Procrustes analysis.
diffFactors-methods Performs differential analysis of chroGPS-factors maps based on Procrustes analysis.
diffGenes Performs differential analysis of chroGPS-genes maps based on Bayesian Correct Classification Rates.
diffGenes-methods Performs differential analysis of chroGPS-genes maps based on Bayesian Correct Classification Rates.
distGPS Compute matrix with pairwise distances between objects. Several GPS metrics are available.
distGPS-class Class '"distGPS"'
distGPS-method Compute matrix with pairwise distances between objects. Several GPS metrics are available.
distGPS-methods Compute matrix with pairwise distances between objects. Several GPS metrics are available.
domainDist Overview of intra and inter-domain distances.
find.fdr Performs differential analysis of chroGPS-genes maps based on Bayesian Correct Classification Rates.
find.threshold Performs differential analysis of chroGPS-genes maps based on Bayesian Correct Classification Rates.
geneSetGPS Highlight point (gene) position over a Multi-dimensional Scaling plot.
geneSetGPS-method Highlight point (gene) position over a Multi-dimensional Scaling plot.
geneSetGPS-methods Highlight point (gene) position over a Multi-dimensional Scaling plot.
getPoints Metric and non-metric Multidimensional Scaling for a distGPS object.
getPoints-method Metric and non-metric Multidimensional Scaling for a distGPS object.
getR2 Metric and non-metric Multidimensional Scaling for a distGPS object.
getR2-method Metric and non-metric Multidimensional Scaling for a distGPS object.
getStress Metric and non-metric Multidimensional Scaling for a distGPS object.
getStress-method Metric and non-metric Multidimensional Scaling for a distGPS object.
getURL Retrieve file from URL.
gff2RDList Retrieve binding site information from GFF3 files.
gps2xgmml Export an 'mds' object to Cytoscape .xgmml format
gps2xgmml-method Export an 'mds' object to Cytoscape .xgmml format
hclust-class Class '"clusGPS"'
is.adj Metric and non-metric Multidimensional Scaling for a distGPS object.
is.adj-method Metric and non-metric Multidimensional Scaling for a distGPS object.
m.origs Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
mds Metric and non-metric Multidimensional Scaling for a distGPS object.
mds-class Class '"mds"'
mds-method Class '"mds"'
mds-method Metric and non-metric Multidimensional Scaling for a distGPS object.
mds-methods Metric and non-metric Multidimensional Scaling for a distGPS object.
mergeClusters Unsupervised cluster merging based on their observed overlap with automatic changepoint detection.
mergeClusters-method Unsupervised cluster merging based on their observed overlap with automatic changepoint detection.
mergeClusters-methods Unsupervised cluster merging based on their observed overlap with automatic changepoint detection.
mergeReplicateList Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
mergeReplicateMatrix Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
mergeReplicateMDS Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
mergeReplicates Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
mergeReplicates-method Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
mergeReplicates-methods Merges information from epigenetic replicates at factor, gene and chroGPS MDS map level.
plot-method Class '"clusGPS"'
plot-method Class '"mds"'
plot-method Metric and non-metric Multidimensional Scaling for a distGPS object.
plotContour Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
plotDiffGenes Performs differential analysis of chroGPS-genes maps based on Bayesian Correct Classification Rates.
procrustesAdj Use Procrustes to adjust an MDS map containing samples obtained under different conditions, e.g. technology or genetic backgrounds.
procrustesAdj-method Use Procrustes to adjust an MDS map containing samples obtained under different conditions, e.g. technology or genetic backgrounds.
procrustesAdj-methods Use Procrustes to adjust an MDS map containing samples obtained under different conditions, e.g. technology or genetic backgrounds.
profileClusters Assess epigenetic profiles for genes present in each cluster as obtained by the 'clusGPS' function.
rankFactorsbyDomain Function to help selecting candidate epigenetic factors based on Epigenetic Domain cohesion/separation.
rankFactorsbyDomain-method Function to help selecting candidate epigenetic factors based on Epigenetic Domain cohesion/separation.
rankFactorsbyDomain-methods Function to help selecting candidate epigenetic factors based on Epigenetic Domain cohesion/separation.
rankFactorsbyProfile Function to help selecting candidate epigenetic factors based on their predictive capabilities.
repliSeq Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2 Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2.tab Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2.wt Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2names Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2Seq Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
s2SeqNames Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
show-method Class '"clusGPS"'
show-method Class '"distGPS"'
show-method Class '"mds"'
show-method Class '"splitDistGPS"'
splidDistGPS-class Class '"splitDistGPS"'
splitDistGPS-class Class '"distGPS"'
splitDistGPS-method Compute matrix with pairwise distances between objects. Several GPS metrics are available.
splitDistGPS-method Class '"splitDistGPS"'
tabClusters Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
tabClusters-method Computation of cluster density estimates for cluster contour representation and correct-classification rates (cluster robustness). A pre-computed clustering of elements used in the map has to be given as an input, which is useful to explore results using different clustering algorithms and methodologies (top-down, bottom-up, etc).
toydists Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
uniqueCount Compute matrix with pairwise distances between objects. Several GPS metrics are available.