twilight(xin, lambda = NULL, B = 0, boot.ci = 0.95, clus = NULL, verbose = TRUE)
twilight
object. makeCluster(clus,...)
in library(snow)
. If specified, bootstrapping is performed in parallel. No checks on clus
are performed. Please make sure that makeCluster(clus)
works properly in your environment. twilight
object consisting of a data.frame
named result
with variables
pi0
.boot.ci
-bootstrap confidence bound.boot.ci
-bootstrap confidence bound.pvalue
.
NOTE: Library(snow) has to be loaded manually. It is not loaded as part of 'suggests' or 'depends' because it is only available under UNIX. If twilight does not work with the current version of snow, please send a report.
Scheid S and Spang R (2005): twilight; a Bioconductor package for estimating the local false discovery rate, Bioinformatics 21(12), 2921--2922.
Scheid S and Spang R (2006): Permutation filtering: A novel concept for significance analysis of large-scale genomic data, in: Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M (Eds.): Research in Computational Molecular Biology: 10th Annual International Conference, Proceedings of RECOMB 2006, Venice, Italy, April 2-5, 2006. Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347.
Storey JD and Tibshirani R (2003): Statistical significance for genomewide studies, PNAS 100(16), 9440--9445.
twilight.pval
, plot.twilight
, exfdr
### twilight object created with B=1000 bootstrap samples
data(exfdr)
print(exfdr)
plot(exfdr)
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