rcA {rxSeq} | R Documentation |
Reformatted data for autosomal set to be used as input to process function
Description
This is an object of type readCounts provides with example of experimental data for a subset of autosomal genes. The full model requires a combination of total read counts (y) - all the reads belonging for a gene, and finding out which of these reads we can specifically attribute to allele A or allele B - allele specific counts (n), separately the reads attributed specifically to allele B (n0B). In autosomes Xce effect is absent, so it would be set to NULL for this dataset. Also, it includes the other data pieces to fit the model: kappas - total number of counts for each mouse, on log scale, index - specifying which cross each mouse belongs to, and geneids - Ensembl ids of genes. Such values also can be simulated with simRX can be fitted using process with appropriate options chrom="X" and field model to be either "full" or "short".
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 vasyl@unc.edu
See Also
Examples
# see total read counts (TReC) for first 2 X chromosome genes of a data example:
rcX