PLNobject: PLN object

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

Description

Create a PLN object, a list containing a read count matrix ‘count’ and sample description matrix ‘sample’.

Usage

PLNobject(count,conditionNumber)

Arguments

count

This is a matrix containing the read counts of R*I samples at J genes (R is the number of conditions in each matched sample set and I is the number of sample sets). Here columns 1 through I are for I independent samples from condition 1, columns I+1 through 2I are for I samples from condition 2 matched by samples 1 through I, ... , columns (R-1)*I+1 through R*I are for I samples from condition R matched by samples 1 through I.

conditionNumber

Number of conditions.

Value

d$count	Origninal read count matrix
d$conditionNumber	The number of conditions
d$sample	A matrix of sample information: ‘SampleName’, ‘TotalCount’, ‘MedianCount’

Examples

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

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