rowlist {LMGene}R Documentation

Gene name listing function

Description

This function makes significant gene list for a specified factor, where genes are selected as significant by the given p-values and significance level.

Usage

rowlist(genemat, effnum, apvlist, level, posterior = TRUE)

Arguments

genemat A matrix data of array
effnum Factor number
apvlist A vector with FDR adjusted p-value
level Significance level
posterior TRUE, if adjusted p-values are to be computed with Posterior method.

Details

genemat is an n-by-p matrix of expression values effnum is the coumn number for the effect of interest apvlist is a matrix of p-values from pvadjust or genediff the routine returns a list of genes whose FDR p-value is less than level using either individual gene or posterior MSE's. This function returs gene names if rownames(genemat) is not null, or gene numbers otherwise.
level indicates False Discovery Rate. e.g.) level 0.05 means 5

Value

genelist A vector containing gene names if rownames(genemat) is not null, or gene numbers otherwise

Author(s)

David Rocke and Geun-Cheol Lee

References

David M. Rocke (2004), Design and analysis of experiments with high throughput biological assay data, Seminars in Cell & Developmental Biology, 15, 703-713.

http://www.idav.ucdavis.edu/~dmrocke/

See Also

LMGene, rowaov

Examples

#library
library(Biobase)
library(LMGene)

#data
data(Smpd)
data(vlist)
LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist)

pvlist<-genediff(LoggedSmpd0)
apvlist<-pvadjust(pvlist)

genelist<-rowlist(LoggedSmpd0@exprs,3,apvlist,0.01)
genelist


[Package LMGene version 1.0.0 Index]