GeneSelect: Selection of informative geneset

In GSAQ: Gene Set Analysis with QTL

Description

The function returns the informative geneset from the high dimensional gene expression data using a proper statistical technique.

Usage

GeneSelect(x, y, s, method)

Arguments

x	x is a N x m gene expression data matrix (must be data frame) and row names as gene names, where, N represents the number of genes in the whole gene space and m is number of samples.
y	y is a m by 1 vector representing the sample labels, is according to the different stress conditions for two class problem (must be 1: stress/-1: control)
s	s is a numeric constant representing the number of genes to be selected from the large pool of genes/ gene space.
method	method is a character string indicating which method for informative gene selection is to be used. One of method "t-score" (default), "F-score", "MRMR", "BootMRMR" can be abbreviated and used.

Value

The function returns the informative geneset using a particular method from the high dimensional gene expression data.

Author(s)

Samarendra Das

Examples

data(rice_salt)
x=as.data.frame(rice_salt[-1,])
y=as.numeric(rice_salt[1,])
GeneSelect(x, y, s=50, method="t-score")$selectgenes

Example output

 [1] "OsAffx.18823.1.S1_at"   "Os.52357.1.S1_at"       "Os.57545.1.S1_x_at"    
 [4] "Os.27237.1.A1_a_at"     "Os.15665.1.S1_at"       "Os.11919.1.S1_at"      
 [7] "OsAffx.5266.1.S1_x_at"  "OsAffx.28630.1.S1_at"   "Os.26728.3.S1_at"      
[10] "OsAffx.14372.2.S1_at"   "Os.57517.1.S1_at"       "OsAffx.6163.1.S1_x_at" 
[13] "Os.19822.1.S1_at"       "OsAffx.9461.1.S1_at"    "OsAffx.31668.1.S1_at"  
[16] "OsAffx.24056.2.S1_at"   "Os.24287.1.A1_at"       "Os.8957.1.S1_at"       
[19] "Os.50892.1.S1_at"       "OsAffx.3973.1.S1_x_at"  "Os.6141.1.S1_s_at"     
[22] "OsAffx.5284.1.S1_at"    "OsAffx.7406.1.S1_at"    "Os.49199.1.S1_at"      
[25] "Os.7388.2.S1_x_at"      "Os.17465.1.S1_at"       "OsAffx.15802.1.S1_at"  
[28] "Os.14770.1.S1_at"       "Os.53064.1.S1_at"       "OsAffx.25841.1.S1_at"  
[31] "OsAffx.17895.1.S1_at"   "OsAffx.30771.1.S1_at"   "Os.27839.1.S1_at"      
[34] "Os.23660.1.S2_at"       "OsAffx.21997.3.S1_x_at" "Os.8545.1.S1_at"       
[37] "Os.52757.1.S2_at"       "Os.52011.1.S1_at"       "Os.49488.1.S1_at"      
[40] "OsAffx.12573.1.S1_s_at" "Os.11237.1.S1_at"       "Os.13516.1.S1_at"      
[43] "OsAffx.8465.1.S1_x_at"  "Os.24329.1.A1_at"       "OsAffx.28033.1.S1_x_at"
[46] "OsAffx.22281.1.S1_at"   "Os.9515.3.S1_x_at"      "OsAffx.5106.1.S1_at"   
[49] "Os.53924.1.S1_at"       "OsAffx.18359.1.S1_at"  

GSAQ documentation built on May 2, 2019, 9:34 a.m.