eLNNpaired (version 0.2.3)

samrOneClass:

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.

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))