pcorfdrci.inv {GeneNT}R Documentation

Inverse screening procedure based on Kendall correlation coefficient

Description

The inverse screening procedure is presented in our the paper below. It allows the FDR p-value of a gene pair's strength of association measured using partial correlation coefficient to be computed

Usage

pcorfdrci.inv(pcormin)

Arguments

pcormin partial correlation threshold

Details

Please refer to Zhu et al. below for detail.

Value

This function returns a list of fdr adjusted p-values.

Author(s)

Dongxiao Zhu (http://www-personal.umich.edu/~zhud)

References

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

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). Submitted.

Schäfer, J., and K. Strimmer. (2004) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics, 1, 1-13.

See Also

corfdrci.inv

Examples

# load GeneNT and GeneTS library
library(GeneTS)
library(GeneNT)

#EITHER use the example dataset
data(dat) 
#OR use the following if you want to import external data 
#dat <- read.table("gal.txt", h = T, row.names = 1) 
#Note, data matrix name has to be "dat"
#Subset data to run faster
dat <- dat[1:10,]
#Set MAS level pcormin = 0.8, calculate fdr adjusted p-values. 
#fdrp8 <- pcorfdrci.inv(0.8)                                   

[Package GeneNT version 1.2 Index]