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. |