kendallfdrci {GeneNT} | R Documentation |
This function implement the two-stage screening procedure based on Kendall correlation coefficient. Specifying a pair of FDR and MAS criteria, the algorithm provides an initial co-expression discovery that controls only FDR, which is then followed by a second stage co-expression discovery which controls both FDR and MAS.
kendallfdrci(Q, cormin, method)
Q |
The significant level |
cormin |
The specified minimum acceptable strength of association measured using Kendall correlation coefficient |
method |
The multiple comparison adjustment methods, eg, "BH" (for independent tests) and "BY" (for general dependent tests) |
The data matrix file must be in the right format. The first row must be one shorter than the rest rows. The first column must be gene names.
The function returns a list of gene pairs that satisfies the FDR and MAS criteria simultaneously measured by Kendall correlation coefficient.
kG1 |
The gene pairs that passes Stage I (FDR only) screening |
kG2 |
The gene pairs that passed both Stage I (FDR) and II (MAS) screenings |
Dongxiao Zhu (http://dongxiaozhu.googlepages.com/home)
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. Hollander M. and Wolfe D.A. (1999). Nonparametric Statistical Methods, New York: Wiley.
## load GeneNT library library(GeneNT) ## load example dataset data(dat) ## Note, data matrix name has to be "dat" g2 <- kendallfdrci(0.2, 0.5, "BY") kG1 <- g2$kG1 ## kG2 contains gene pairs that passed two-stage screening kG2 <- g2$kG2