BEST.pearson {GeneNT}R Documentation

BLAST type search for similar co-expressions with controlled FDR and MAS using Pearson correlation statistic

Description

This function implement the BLAST type two-stage screening procedure based on Pearson correlation coefficient. Specifying a pair of FDR and MAS criteria, and a seed gene, the algorithm screens a seeded gene cluster with controlled FDR and MAS.

Usage

BEST.pearson(gene.name, Q, cormin, method)

Arguments

gene.name The "seed" gene name
Q The significant level
cormin The specified minimum acceptable strength of association measured by Pearson correlation statistic
method The multiple comparison adjustment methods, eg, "BH" (for independent tests) and "BY" (for general dependent tests)

Details

The data matrix file must be in the right format. The first row (header) must be one shorter than the rest rows. The first column must be gene names.

Value

The function returns a seeded gene cluster that satisfies the FDR and MAS criteria measured by Pearson correlation coefficient simultaneously.

bpG1 The gene pairs that passes Stage I (FDR only) screening
bpG2 The gene pairs that passed both Stage I (FDR) and II (MAS) screenings

Author(s)

Dongxiao Zhu (http://dongxiaozhu.googlepages.com/home)

References

Zhu, D., Hero, A.O., Qin, Z.S. and Swaroop, A. High throughput screening of co-expressed gene pairs with controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). J Comput Biol, 12, 1027-1043.

Fisher, R.A. (1921). On the 'probable error' of a coefficient of correlation deduced from a small sample. Metron, 1, 1–32.

See Also

BEST.kendall

Examples

## Load GeneNT library
library(GeneNT)

## load example dataset
data(dat) 
## Note, data matrix name has to be "dat"

## use (FDR, MAS) criteria (0.2, 0.5) and seed gene "GAL7" as example to screen gene pairs 
## use "BY" procedure to do multiple comparison adjustment
g4 <- BEST.pearson("GAL7", 0.2, 0.5, "BY")  
bpG1 <- g4$bpG1

## bpG2 contains gene pairs that passed two-stage screening
bpG2 <- g4$bpG2  

[Package GeneNT version 1.4 Index]