get.tausB {rxSeq} | R Documentation |
Produce Xce estimates for mice with allele specific reads
Description
Xce estimation for mice with allele specific reads.
Usage
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
Examples
# Estimating XCE effect for each mouse for X chromosome
get.tausB(n=data.X$n, n0B=data.X$n0B, geneids=data.X$geneids)
[Package rxSeq version 0.99.3 Index]