get.tausB: Produce _Xce_ estimates for mice with allele specific reads

Description Usage Arguments Value Author(s) See Also Examples

Description

Xce estimation for mice with allele specific reads.

Usage

1
get.tausB(n, n0B, geneids, min.cnt=50, exclude.prop=.05, Xist.ID="ENSMUSG00000086503")

Arguments

n

vector of allele specific counts for each mouse

n0B

vector of allele specific counts for allele B

geneids

gene IDs

min.cnt

minimum number of allele specific counts

exclude.prop

minimum proportion of allele specific counts for each allele

Xist.ID

and ID of Xist, to exclude it from estimating Xce, since Xce would 1-tausB

Value

output - matrix of 4 rows:

med.tauB

taus estimated via median

ave.tauB

taus estimated via percent of allele B counts

all.genes

number of genes that had passed minimum count

used.genes

number of genes that had required percent of each allele

each column represent respective mouse.

Author(s)

Vasyl Zhabotynsky vasyl@unc.edu

See Also

process,nLogLik, data.X, rcX.

Examples

1
2
# Estimating XCE effect for each mouse for X chromosome
get.tausB(n=data.X$n, n0B=data.X$n0B, geneids=data.X$geneids)

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