clusterStat: generate statistics on sizes of clusters

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description

'cluster.sizestat' is used to do simple statistics on sizes of clusters generated by 'clusterCMP'. It will return a dataframe which maps a cluster size to the number of clusters with that size. It is often used along with 'cluster.visualize'.

Usage

clusterStat(cls, cluster.result = 1)

Arguments

cls	The clustering result returned by 'clusterCMP'.
cluster.result	If multiple cutoff values are used in clustering process, this argument tells which cutoff value is to be considered here.

Details

'cluster.sizestat' depends on the format that is returned by 'clusterCMP' - it will treat the first column as the indecies, and the second column as the cluster sizes of effective clustering. Because of this, when multiple cutoffs are used when 'clusterCMP' is called, 'cluster.sizestat' will only consider the clustering result of the first cutoff. If you want to work on an alternative cutoff, you have to manually reorder/remove columns.

Value

Returns A data frame of two columns.

Author(s)

Min-feng Zhu <[e-mail]>

References

...

Examples

data(sdfbcl)
apbcl <- convSDFtoAP(sdfbcl)

cluster <- clusterCMP(db = apbcl, cutoff = c(0.65, 0.5))
clusterStat(cluster[, c(1, 2, 3)])
clusterStat(cluster[, c(1, 4, 5)])

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.