mbetattest: Performance of multiple beta t-test on simulated data

In Yuande/MBttest: Multiple Beta t-Tests

Performance of multiple beta t-test on simulated data

Description

This function is to peform multiple beta t-test method on real data. The result lists geneid or isoformid, gene name, the other information, t-value, p-value, adjusted p-value, adjusted alpha value, rho (ρ), and symb. All these lists are ordered by absolution of t-values.

Usage

mbetattest(X, na, nb, W, alpha=0.05, file)

Arguments

X	count data of RNA reads with na replicates in condition A ans nb replicates in condition B.
na	number of replicate libraries in condition A.
nb	number of replicate libraries in condition B.
W	numeric parameter, called omega (ω) that is a constant determined by null simulation.
alpha	the probabilistic threshold. User can set alpha (α)= 0.05 or 0.01 or the other values. Defalt value is 0.05
file	a csv file. User needs to give file name and specify direction path. But if user uses setwd function, drive is not necessarily specified in file.

Details

t-statistic is defined as t-statistic multiplied by (rho/omega), that is,

T=t\times \frac{ρ}{ω}

where

t=\frac{(P_A-P_B)}{√(V_A+V_B)}

ρ=√{ψ ζ}

where

ψ =max(\frac{min(X_A)}{max(X_B)+1},\frac{min(X_B)}{max(X_A)+1})

ζ=log(1+\frac{\bar{X}σ^2+1}{\bar{X}_Aσ^2_A+\bar{X}_Bσ^2_B+1})

ω is a constant as threshold estimated from null data.

Value

return a dat list: the data ordered by abs(t) contain information cloumns, data columns, t-values, rho and symb that are used to make heatmap and MAplot.

Author(s)

Yuan-De Tan [e-mail]

References

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

smbetattest.

Examples

data(jkttcell) 

dat<-mbetattest(X=jkttcell[1:1000,],na=3,nb=3,W=1,alpha=0.05,file="jurkat_NS_48h_tag_mbetattest.csv")

Yuande/MBttest documentation built on Aug. 25, 2022, 12:58 a.m.