getOrder {affycoretools}R Documentation

Order Probesets Based on Fold Change Values

Description

This function is used to create a list containing the correct order to output a set of probesets based on the fold change values for those probesets. This is an internal function and is not intended to be called by end users.

Usage

getOrder(fcList, order.by)

Arguments

fcList A list of named lists, generally produced by a call to makeFCList
order.by One of 'sum', 'max', 'median', or 'mean'. This orders the output for those tables that have multiple fold change values based on the summary statistic chosen. Defaults to 'sum'.

Details

The purpose of this function is to come up with some ordering for probesets that will be ouput by a call to vennSelectFC. The ordering for probesets unique to a given comparison is simple, since there is only one fold change to be considered. However, when there are more than one comparison, we have to decide how the probesets should be ordered. The choices available include those that seemed reasonable to me when I wrote this function. Presumably there are other reasonable choices that may need to be included.

Author(s)

James W. MacDonald <jmacdon@med.umich.edu>


[Package affycoretools version 1.8.1 Index]