calcFactornew {methylMnM} | R Documentation |
Amends of TMM normalization for our methond.
calcFactornew(obs, ref, m, k, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10)
obs |
Counts of treatment sample. |
ref |
Counts of control sample. |
m |
The number of CpG in each bin. |
k |
The number of MRE-CpG in each bin. |
logratioTrim |
amount of trim to use on log-ratios ("M" values) |
sumTrim |
amount of trim to use on the combined absolute levels ("A" values) |
doWeighting |
logical, whether to compute (asymptotic binomial precision) weights |
Acutoff |
cutoff on "A" values to use before trimming |
A real value larger than 0.
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
d <- matrix( rpois(1000, lambda=5), nrow=200 ) m<-rep(1,nrow=200 ) k<-rep(1,nrow=200 ) f <- calcFactornew(d[,2], d[,1], m, k, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10)