compute.pod: A function to compute the proportion of deviation from...

In iCluster: Integrative clustering of multiple genomic data types

Description

A function to compute the proportion of deviation from perfect block diagonal matrix.

Usage

compute.pod(fit)

Arguments

fit	A iCluster object

Value

pod	proportion of deviation from perfect block diagonal matrix

Author(s)

Ronglai Shen [e-mail]

References

Ronglai Shen, Adam Olshen, Marc Ladanyi. (2009). Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906-2912.

See Also

iCluster,iCluster2, plotiCluster

Examples

# library(iCluster)
# data(breast.chr17)
# fit=iCluster(breast.chr17, k=4, lambda=c(0.2,0.2))
# plotiCluster(fit=fit, label=rownames(breast.chr17[[2]]))
# compute.pod(fit)

Example output

Loading required package: lattice
Loading required package: caTools
Loading required package: gdata
sh: 1: /usr/bin/perl: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: ‘gdata’

The following object is masked from ‘package:stats’:

    nobs

The following object is masked from ‘package:utils’:

    object.size

The following object is masked from ‘package:base’:

    startsWith

Loading required package: gtools
Loading required package: gplots
Registered S3 method overwritten by 'gplots':
  method         from 
  reorder.factor gdata

Attaching package: ‘gplots’

The following object is masked from ‘package:gdata’:

    reorder.factor

The following object is masked from ‘package:stats’:

    lowess

Loading required package: parallel
Warning message:
In system(cmd, intern = TRUE) :
  running command ''/usr/bin/perl' '/usr/lib/R/site-library/gdata/perl/supportedFormats.pl'' had status 126

iCluster documentation built on May 2, 2019, 11:25 a.m.