rxSeq (version 0.99.3)

readCounts: A list object that should be used as input to optimization process function.

Description

It should contain at least total read counts (TReC) and classification of crosses 1 to 8. To fit the full model should also have appropriate allele specific counts n and n0B. Also is used along with results of optimization as input to nLogLik function if one needs to calculate Hessian matrix.

Value

See Also

process,nLogLik, simRX.

Examples

# see total read counts (TReC) for first 2 X chromosome genes of a data example:
rcA = readCounts(index=data.A$index, y=data.A$y[1:2,], n=data.A$n[1:2,], n0B=data.A$n0B[1:2,], 
                 kappas=data.A$kappas, geneids=data.A$geneids[1:2])