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chroGPS (version 1.16.0)

chroGPS: visualizing the epigenome

Description

We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds.

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Version

Version

1.16.0

License

GPL (>=2.14)

Maintainer

Oscar Reina

Last Published

February 15th, 2017

Functions in chroGPS (1.16.0)

gff2RDList

Retrieve binding site information from GFF3 files.
domainDist

Overview of intra and inter-domain distances.
mergeClusters

Unsupervised cluster merging based on their observed overlap with automatic changepoint detection.
mds

Metric and non-metric Multidimensional Scaling for a distGPS object.
mds-class

Class "mds"
profileClusters

Compute enrichment/depletion ratio for the observed epigenetic profiles in epigenetic clusters.
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).
adjustPeaks

Adjust peak width so that samples obtained under different conditions become comparable.
geneSetGPS

Highlight point (gene) position over a Multi-dimensional Scaling plot.
distGPS-class

Class "distGPS"
procrustesAdj

Use Procrustes to adjust an MDS map containing samples obtained under different conditions, e.g. technology or genetic backgrounds.
boostMDS

Improve goodness-of-fit of a given MDS solution in terms of R-square.
s2

Sample binding site and related data from S2 and BG3 cell lines in Drosophila melanogaster.
gps2xgmml

Export an 'mds' object to Cytoscape .xgmml format
clusGPS-class

Class "clusGPS"
splitDistGPS-class

Class "splitDistGPS"
distGPS

Compute matrix with pairwise distances between objects. Several GPS metrics are available.
addVar

Plot vector of a quantitative variable over a MDS map.
getURL

Retrieve file from URL.