samrOneClass: A Wrapper Function of samr for Paired Data

In eLNNpaired: Model-Based Gene Clustering for Genomics Data from Paired/Matched Designs

Description

A wrapper function of samr for paired data.

Usage

samrOneClass(
  es, 
  fdr.output = 0.05, 
  nperms = 100)

Arguments

es	An ExpressionSet object stores within-pair log2 difference.
fdr.output	fdr cutoff for output in significant genes table. (see SAM function in samr package.
nperms	Number of permutations used to estimate false discovery rates. (see samr function in samr package).

Value

A list of 5 elements:

samr.obj	object returned by samr function
del	estimated cutoff value required by samr.compute.siggenes.table function. See the source code of SAM function
delta.table	object returned by samr.compute.delta.table
siggenes.table	object returned by samr.compute.siggenes.table function
memGenes	probe cluster membership. 1 indicates over-expressed probes; 2 indicates under-expressed probes; 3 indicates non-differentially expressed probes
memGenes2	2-cluster probe cluster membership. 1 indicates differentially-expressed probes; 0 indicates non-differentially-expressed probes.

Author(s)

Yunfeng Li <[e-mail]> and Weiliang Qiu <[e-mail]>

References

Li Y, Morrow J, Raby B, Tantisira K, Weiss ST, Huang W, Qiu W. (2017), <doi:10.1371/journal.pone.0174602>

Examples

set.seed(100)
G = 500
n = 10

delta_1 = -0.8184384  
xi_1 = -1.1858546 
lambda_1 = -10.6309216  
nu_1 = -3.5536255  

delta_2 = -0.8153614  
xi_2 = -1.4120148 
lambda_2 = -13.1999427  
nu_2 = -3.3873531   

lambda_3 = 0.7597441  
nu_3 = -2.0361091 

psi = c(delta_1, xi_1, lambda_1, nu_1,
        delta_2, xi_2, lambda_2, nu_2,
        lambda_3, nu_3)
t_pi = c(0.08592752, 0.07110449)

c1 = qnorm(0.95)
c2 = qnorm(0.05)

E_Set = gen_eLNNpaired(G, n, psi, t_pi, c1, c2)

result = samrOneClass(es=E_Set)

print(table(result$memGenes, fData(E_Set)$memGenes.true))
print(table(result$memGenes2, fData(E_Set)$memGenes2.true))

eLNNpaired documentation built on May 29, 2017, 12:04 p.m.