# chroGPS: visualizing the epigenome

## Documentation for package ‘chroGPS’ version 1.12.0

- 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 | Compute matrix with pairwise distances between objects. Several GPS metrics are available.
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).
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.
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.
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.
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.
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.
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).
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 | Compute enrichment/depletion ratio for the observed epigenetic profiles in epigenetic clusters.
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.