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. |
bg3 |
Sample binding site and related data from Drosophila melanogaster. |
bg3names |
Sample binding site and related data from Drosophila melanogaster. |
boostMDS |
Improve goodness-of-fit of a given MDS solution in terms of R-square. |
clusGPS |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
clusGPS-class |
Class '"clusGPS"' |
clusGPS-method |
Class '"clusGPS"' |
clusGPS-method |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
clusGPS-methods |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
contour2dDP |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
contour3dDP |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
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. |
geneSample |
Sample binding site data from Drosophila melanogaster S2-DSRC cell lines (ChIP-chip), coming from modEncode Release 21. |
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. |
getURL |
Retrieve file from URL. |
gff2RDList |
Retrieve binding site information from GFF3 files. |
hclust-class |
Class '"clusGPS"' |
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. |
plot-method |
Class '"clusGPS"' |
plot-method |
Class '"mds"' |
plot-method |
Metric and non-metric Multidimensional Scaling for a distGPS object. |
plotContour |
Hierarchical clustering (Agglomerative Nesting) of elements based on their input pairwise distances. |
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. |
S2Controls |
Sample binding site data from Drosophila melanogaster S2-DSRC cell lines (ChIP-chip), coming from modEncode Release 21. |
show-method |
Class '"clusGPS"' |
show-method |
Class '"distGPS"' |
show-method |
Class '"mds"' |
show-method |
Class '"splitDistGPS"' |
sl2 |
Sample binding site and related data from Drosophila melanogaster. |
sl2names |
Sample binding site and related data from Drosophila melanogaster. |
sl2seq |
Sample binding site and related data from Drosophila melanogaster. |
sl2seqnames |
Sample binding site and related data from Drosophila melanogaster. |
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"' |
uniqueCount |
Compute matrix with pairwise distances between objects. Several GPS metrics are available. |