chroGPS: navigating through the epigenome

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Documentation for package ‘chroGPS’ version 1.0.1

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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.
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.