LRtest2: Likelihood ratio test for differential expression analysis...

In zhanghfd/PLNseq: PLNseq: A multivariate Poisson lognormal distribution for high-throughput correlated RNA-sequencing read count data

Description

This function calculates log-fold changes, likelihood ratio test statistics, and p-values for a list of genes. This function should be called after cluster-specific correlations are returned by ‘correlationCoefficient’.

Usage

    LRtest2(d,M,use.commonSigma,id)

Arguments

d	This is a PLNseq object.
M	The number of simulations used in Monte-Carlo method for calculating likelihood ratio test statistics.
use.commonSigma	Use common ‘sigma’ (TRUE) or genewise ‘sigma’ (FALSE), with default value ‘FALSE’.
id	A vector consisting of a subset of 1,...,J, with default value 1:J (all genes are analyzed).

Value

LR	Estimation and test results: ‘log-FC’, ‘LR statistic’, ‘p value’.

Examples

    data(lung);
    count = lung[,c(2:4,8:10)];
    d = PLNobject(count,conditionNumber=2);
    d = sizeFactor(d,maxCount=2e3);

    ##  Not run:
    ##  d = commonSigma(d);
    ##  J = nrow(count);
    ##  J1 = round(J/2);
    ##  d$commonCorrelation = FALSE;
    ##  d$cluster = c(rep(1,J1),rep(2,J-J1));
    ##  d = correlationCoefficient(d);
    ##  d = genewiseSigma(d);
    ##  d = LRtest2(d,M=3e4,use.commonSigma=FALSE,id=1:100);

zhanghfd/PLNseq documentation built on May 4, 2019, 10:16 p.m.