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ssa: Simultaneous Signal Analysis

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

6

Version

1.3.0

License

GPL-3

Maintainer

Dave Zhao

Last Published

January 14th, 2019

Functions in ssa (1.3.0)

Nonparametric empirical Bayes classifier without annotations; training

nebula.bin.train

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

Latent dependency detection

Nonparametric false simultaneous discovery rate control, two thresholds

Max test for detecting simultaneous signals

nebula.chisq.bin.predict

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

Nonparametric false simultaneous discovery rate control, two thresholds -- report all thresholds

Polygenic risk score; prediction

nebula.chisq.bin.train

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

Polygenic risk score; prediction for classifier trained with CV

Nonparametric empirical Bayes classifier without annotations; prediction

nebula.chisq.train

Nonparametric empirical Bayes classifier using latent annotations: chi-square test statistics; training

nebula.chisq.predict

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

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

Trivariate NPMLE

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

Polygenic risk score (given only allele frequencies); training

Univariate NPMLE

Nonparametric empirical Bayes classifier using latent annotations: wrapper function; training

Nonparametric false simultaneous discovery rate control

nebula.bin.predict

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

Bivariate NPMLE