Description Value Author(s) See Also Examples
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.
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) |
Vasyl Zhabotynsky vasyl@unc.edu
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