order.by.am {UCS}R Documentation

Sort Rows of a Data Set by Association Scores (base)


Sort the rows of a data set according to the annotated scores of an association measure (in descending order). Ties in the ordering are broken randomly by default, using the random association measure to yield a reproducible ordering.


order.by.am(ds, am, randomise=TRUE)


an integer vector of row numbers, which can be used as a row index for the data set object With randomise=TRUE, the data set must contain a variable named am.random, which is used to break ties in the ordering. Otherwise, tied rows are arranged according to their ID values, and the corresponding id variable must be annotated in the data set.

The random association measure is used for breaking ties (rather than random numbers generated on the fly) in order to ensure that the ordering is reproducible. If this measure has not been annotated in a data set file, you can easily add the required variable to a data set ds with the command

    ds$am.random <- runif(nrow(ds))
You should probably use set.seed to ensure a reproducible ordering. read.ds.gz, add.ranks UCS
ds a UCS data set
am a character string giving the name of a single association measure
randomise if TRUE, ties in the ordering are broken randomly (default). Otherwise, the tied rows are arranged according to their id values. See below for details.

[Package UCS version 0.5 Index]