PLN_ANOVA: Differential expression analysis based on a rank-reduced...

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

Description

This function returns the u estimates and DE analysis results including estimated log-fold changes (‘logFoldChange’) and the correponding estimated standard errors (‘sd.logFoldChange’), and DE test p-values (‘p.value’).

Usage

    PLN_ANOVA(d,n.top=1e3)

Arguments

d	This is a PLNseq object.
n.top	The number of genes used to estimated u and v parameters.

Value

d$ANOVA

A list containg ‘u’, ‘logFoldChange’, ‘sd.logFoldChange’, and ‘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);
    ##  d = genewiseSigma(d);
    ##  d$commonCorrelation = TRUE;
    ##  d = correlationCoefficient(d);
    ##  d = PLN_ANOVA(d,n.top=1e3);

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