laptopTable: Table of Top Genes from Laplace Linear Model Fit

In lapmix: Laplace Mixture Model in Microarray Experiments

Description

Extract a table of the top-ranked genes from a Laplace mixture model fit.

Usage

laptopTable(res, number=res$med.number, sort.by='L')

Arguments

res	the output from the lapmix.Fit routine
number	how many genes to pick out; if missing: number is determined by the median rule
sort.by	character string specifying statistic to sort the selected genes by in the output data.frame.

Details

This function summarizes a Laplace mixture model fit object produced by lapmix.Fit by selecting the top-ranked genes according to the posterior log-odds or M-values.

The sort.by argument specifies the criterion used to select the top genes. Only two choices at the moment: "M" to sort by the (absolute) coefficient representing the log-fold-change, and "L" to sort by the posterior odds of differential expression under the Laplace mixture model.

Value

A dataframe with a row for the number top genes and the following columns:

M	average log fold change
log.odds	log posterior odds that the gene is differentially expressed

Author(s)

Yann Ruffieux

Examples

#  See lapmix.Fit example

Example output

lapmix documentation built on Nov. 8, 2020, 10:59 p.m.