readCounts {rxSeq}

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

index

vector defining the cross of the mouse, female - AB=1, BA=2, AA=3, BB=4, and male - AB=5, BA=6, AA=7, BB=8. If mice are of only one sex, AB=1, BA=2, AA=3, BB=4.

y

matrix of TReC counts. Note, the expected input assumes that inbred mice will be in the last columns of the table, after the last F1 mouse.

n

matrix of ASE counts for corresponding F1 mouse (classes 1,2,5,6) for corresponding genes.

n0B

matrix of ASE counts belonging for allele B, for correponding genes and mice as in n.

kappas

A parameter, specifying as overall TReC for the mouse, on log scale

tausB

Xce effect: expression of allele B relative to the overall allele specific count for each mouse. Set to NULL in autosomes.

gene.switch

For which genes Xce effect should be switched. Null for autosomes.

geneids

ids of genes, if not provided, rownames of the matrix y will be used

chrom

this field would be set to be "X" since this is dataset for chromosome X

model

set to be "full", can be modified to "short" to run a TReC oply model

geneids

Ensembl gene ids

tech.ctrl

a list of overdispersion boundaries and log(2)

Author(s)

Vasyl Zhabotynsky [e-mail]

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])