hub.pval.cutoff: Identification of hub genes in a Gene Co-expression Network...

In dhga: Differential Hub Gene Analysis

Description

The function returns list of top ranked hub genes under a particular condition/trait

Usage

hub.pval.cutoff(x, beta, m, s, n)

Arguments

x	x is a data frame of gene expression values where rows represent genes and columns represent samples/time point under a particular condition/trait.
beta	beta is a soft threshold parameter determined from the scale free property of biological networks (Gene Co-expression Network).
m	m is a scalar representing sample size and is less than or equal to number of columns in x.
s	s is a scalar representing number of times each of the m samples will be resampled.
n	n is a scalar representing number of top ranked hub genes to be selected under that particular condition/trait

Value

The function returns a vector containing list of top ranked hub genes for that particular condition/trait

Author(s)

Samarendra Das and Baidya Nath Mandal

Examples

data(rice_salt)
x=as.data.frame(rice_salt)
beta=6
m=18
s=80
n=20
hub.pval.cutoff(x, beta, m, s, n)

Example output

Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
 [1] "Os.55524.1.S1_at"     "Os.22029.1.S1_a_at"   "OsAffx.12383.1.S1_at"
 [4] "Os.26770.2.S1_x_at"   "Os.25613.1.A1_at"     "Os.31191.1.S1_at"    
 [7] "OsAffx.25039.1.S1_at" "OsAffx.12783.1.S1_at" "Os.47413.1.S1_at"    
[10] "Os.11272.1.S1_at"     "Os.11555.1.S1_at"     "Os.47737.1.S1_at"    
[13] "Os.51307.1.S1_at"     "OsAffx.26317.1.S2_at" "OsAffx.31756.4.S1_at"
[16] "OsAffx.12433.1.S1_at" "Os.17102.1.S1_at"     "Os.54579.1.S1_s_at"  
[19] "Os.55907.1.S1_at"     "Os.11677.1.S1_x_at"  
attr(,"class")
[1] "Hub Genes"

dhga documentation built on May 2, 2019, 2:13 p.m.