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ssa (version 1.2.1)

Simultaneous Signal Analysis

Description

Procedures for analyzing simultaneous signals, e.g., features that are simultaneously significant in two different studies. Includes methods for detecting simultaneous signals, for identifying them under false discovery rate control, and for leveraging them to improve prediction.

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Version

Install

install.packages('ssa')

Monthly Downloads

19

Version

1.2.1

License

GPL-3

Maintainer

Dave Zhao

Last Published

July 24th, 2016

Functions in ssa (1.2.1)

fsdr_all

False simultaneous discovery rate control -- report all thresholds
fsdr

False simultaneous discovery rate control
expit

Expit function
logit

Logit function
ldd

Latent dependency detection
nebula.bin.predict

Nonparametric empirical Bayes classifier using latent annotations: binary indicators; prediction
maxtest

Max test for detecting simultaneous signals
neb.train

Nonparametric empirical Bayes classifier without annotations; training
neb.predict

Nonparametric empirical Bayes classifier without annotations; prediction
bi.npmle

Bivariate NPMLE
nebula.bin.train

Nonparametric empirical Bayes classifier using latent annotations: binary indicators; training
nebula.train

Nonparametric empirical Bayes classifier using latent annotations: wrapper function; training
nebula.chisq.bin.predict

Nonparametric empirical Bayes classifier using latent annotations: chi-square test statistics and binary indicators; prediction
nebula.chisq.train

Nonparametric empirical Bayes classifier using latent annotations: chi-square test statistics; training
nebula.chisq.bin.train

Nonparametric empirical Bayes classifier using latent annotations: chi-square test statistics and binary indicators; training
prs.predict

Polygenic risk score; prediction
nebula.predict

Nonparametric empirical Bayes classifier using latent annotations: wrapper function; predict
nebula.chisq.predict

Nonparametric empirical Bayes classifier using latent annotations: chi-square test statistics; prediction
uni.npmle

Univariate NPMLE
prs.predict.cv

Polygenic risk score; prediction for classifier trained with CV
prs.train

Polygenic risk score (given only allele frequencies); training
prs.train.cv

Polygenic risk score (given only allele frequencies); training with CV
tri.npmle

Trivariate NPMLE