efs: an R package to Estimate FDR in Sequential genome scan

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install and load

R CMD install efs_0.1.tar.gz -l Rlib
'Rlib' is the destiny folder to install the package. It is possible to put the directory 'Rlib' into the library search path of R by changing the .Rprofile file in the home directory. Or we can just type

.libPaths('\Rlib')

in R. Then the library can be loaded by

library(efs)

Besides the documentation, I think the following 2 examples might help understand the procedure.

Example 1

# load data
data(gs.test,gs.null);

# 'gs.test' contains all LR test statistics from MIM applied to the Brem's yeast data.
# We claimed 5182 QTL for 3367 expression traits with FDR 8%.
# Among them, there are 1242 traits with 2 or more QTL. #
test<-gs.test;
# 'null' contains all null statistics from permutation tests
null<-gs.null;

# estimating p0.
p <- getP0 (test,null,p0.method="efron",p0.quantile=0.25);
#find locfdr for each qtl
f <- find.locfdr (test, null, P0=p);
test <- attach.locfdr(test,f);
# estimate fdr among all positive findings
result <- compute.FDR(test);

Example 2

data(o.test,o.null,m.test,m.null,r.test,r.null);

# replication and modification of John storey's method as published in Plos biology Aug 2005.

# Using F statistics from 2 cycles of sequential genome scans using storey's original method; null statistics are obtained using Churchill's 1994 and 1996 method;
test <- o.test;
null <- o.null;

# Or, using F statistics from M2 that contains only main effects;
test <- m.test;
null <- m.null;

# Or, using F statistics from the restricted search, comparing M2 vs M1 only if F statistic of the the first QTL is larger than 13.94.

test <- r.test;
null <- r.null;

p <- getP0 (test,null, p0.method ="storey");
f <- find.locfdr (test, null, P0=p);
test <- attach.locfdr(test,f);
result <- find.QTL (test,FDR=0.1,n.QTL=2);