correlationCoefficient: Correlation coefficient

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

Description

Estimate correlation coefficient parameter(s) and the corresponding standard error(s) in the multivariate lognormal distribution. The correlation can be either common to all genes or cluster specific (the genes in each cluster share a common correlation).

Usage

correlationCoefficient(d)

Arguments

d	This is a PLNseq object.

Value

d$rho	Correlation coefficient ‘rho’ in the multivariate lognormal distribution
d$rho.se	Standard error of estimated ‘rho’

Examples

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

    ## common correlation
    ## d$commonCorrelation = TRUE;
    ## d = correlationCoefficient(d);

    ## clustered correlation
	  ## d$commonCorrelation = FALSE;
    ## J = nrow(count);
    ## J1 = round(J/2);
    ## d$cluster = c(rep(1,J1),rep(2,J-J1));
    ## d = correlationCoefficient(d);

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