csCluster

csCluster,CuffFeatureSet-method

object


Number of pre-defined clusters to attempt to find.



A logical value whether or not to log-transform the FPKM values prior to clustering.


logMode


Distance function to use when computing cluster solution.  Default "none" will use the Jensen-Shannon distance (JSdist). Provide a function that returns a dist object on rows.


method


Value added to FPKM to avoid log-transform issues.


pseudocount


Returns a ggplot2 plot object with geom_line layer plotting FPKM values over conditions faceted by k-means clustering clusters. (Euclidean).  This is very crude at this point.
This does not return any of the clustering information directly, but if you want it, you can retrieve it from the ggplot object returned.


datasets

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data.  In addition, provides numerous plotting functions for commonly used visualizations.

Loyal A Goff

cummeRbund

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

csCluster function

Source

Number of pre-defined clusters to attempt to find.

A logical value whether or not to log-transform the FPKM values prior to clustering.

Distance function to use when computing cluster solution.  Default "none" will use the Jensen-Shannon distance (JSdist). Provide a function that returns a dist object on rows.

Value added to FPKM to avoid log-transform issues.

Returns a ggplot2 plot object with geom_line layer plotting FPKM values over conditions faceted by k-means clustering clusters. (Euclidean).  This is very crude at this point.
This does not return any of the clustering information directly, but if you want it, you can retrieve it from the ggplot object returned.

csCluster: csCluster

Description

Usage

Arguments

Source

Details

References

Examples