NBBttest-package: Negative Beta Binormail t-Test Package

In NBBttest: Negative Binomial Beta t-Test

Negative Beta Binormail t-Test Package

Description

This package consists of 20 functions, of which betaparametab.R, betaparametVP.R, betaparametw.R, gbetattest.R,betattest.R, mbetattest.R, normalize.R, oddratio.R, pratio.R, omega.R, simulat.R, and smbetattest.R are used to estimate beta, alpha, weight, t-statistics,rho and omega, p-value,and multiple test at gene level or RNA isoform level. NBBplot.R is used to visualize count data of exons within a specified gene in given conditions. QC.R is used to check quality of data, and myheatmap.R,myheatmap2.R, and pathwayheatmap.R are used to show heatmap of differential expressions of DE genes,DE RNA isoform or pathways. Run of mbetattest.R would output beta t-test results including geneid or isoformid, gene name, the other information, t-value, p-value, rho, and omega(W).

Details

Package:	NBBttest
Type:	Package
Version:	1.0.0
Date:	2018-01-11
License:	GPL-3

Author(s)

Yuan-De Tan

Maintainer: Yuan-De Tan [e-mail]

References

Baggerly KA, Deng L, Morris JS, Aldaz CM (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics, 19: 1477-1483.
Yuan-De Tan Anita M. Chandler, Arindam Chaudhury, and Joel R. Neilson(2015) A Powerful Statistical Approach for Large-scale Differential Transcription Analysis. Plos One,10.1371/journal.pone.0123658.

See Also

betaparametab, betaparametVP, betaparametw, gbetattest, betattest, mbetattest, myheatmap, pathwayHeatmap myheatmap2, normalized, oddratio, NBBplot, omega,pratio, QC,simulat, smbetattest

Examples

data(jkttcell) 	
res<-mbetattest(X=jkttcell[1:100, ], nci=7, na=3, 
nb=3, alpha=0.05, norm="yes", side="both", 
level="isoform",padjust_methods="fdr",C=0)

NBBttest documentation built on May 30, 2022, 1:05 a.m.