data.X {rxSeq}

Sample data example for X chromosome genes

Description

This data set 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). Also, tausB - is the Xce effect for each F1 mouse, which specifies the proportion of allele specific reads belonging to allele B. 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. They, as well as the datasets simulated with simRX can be fitted using proc.trecase.X or proc.trec.X.

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. Use some allele specific counts to estimate the effect.

geneids

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

index

index defining which mouse belongs to which cross

y

modified total read counts

n

modified allele specific counts

n0B

modified allele specific coutns, belonging to allele B

kappas

offset, defining a library size for each mouse

tausB

Xce effect for each mouse, for a given cross

geneids

Ensembl gene ids

Author(s)

Vasyl Zhabotynsky [e-mail]

See Also

process,readCounts.

Examples

# see total read counts (TReC) for first 2 X chromosome genes of a data example:
data.X$y[1:2,]