rcA: Reformatted data for autosomal set to be used as input to...

In rxSeq: Combined Total and Allele Specific Reads Sequencing Study

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 [e-mail]

See Also

process,readCounts, simRX.

Examples

# see total read counts (TReC) for first 2 X chromosome genes of a data example:
rcX

rxSeq documentation built on May 1, 2019, 11:31 p.m.