VLMC (version 1.3-13)

bnrf1: BNRF1 Gene DNA sequences: Epstein-Barr and Herpes

Description

Two gene DNA data ``discrete time series'', [object Object],[object Object]

Usage

data(bnrf1)

format

The EB sequence is of length 3954, whereas the HV has 3741 nucleotides. Both are Rfactors with the four levels c("a","c","g","t").

source

See the references, data are online at http://anson.ucdavis.edu/~shumway/tsa.html

References

Shumway, R. and Stoffer, D. (2000) Time Series Analysis and its Applications. Springer Texts in Statistics.

Examples

data(bnrf1)
bnrf1EB[1:500]
table(bnrf1EB)
table(bnrf1HV)
n <- length(bnrf1HV)
table(t = bnrf1HV[-1], "t-1" = bnrf1HV[-n])

plot(as.integer(bnrf1EB[1:500]), type = "b")
ftable(table( t = bnrf1HV[-(1:2)],
              "t-1" = bnrf1HV[-c(1,n)],
              "t-2" = bnrf1HV[-c(n-1,n)]))
 lag.plot(jitter(as.ts(bnrf1HV)),lag = 4, pch = ".")

## Simplistic gene matching:
percent.eq <- sapply(0:200,
           function(i) 100 * sum(bnrf1EB[(1+i):(n+i)] ==  bnrf1HV))/n
plot.ts(percent.eq)