# chroGPS2: Generation, visualization and differential analysis of epigenome maps

## Documentation for package ‘chroGPS’ version 2.2.0

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

## Help Pages

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.