VLMC (version 1.4-4)

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

Description

Two gene DNA data ``discrete time series'',

bnrf1EB

the BNRF1 gene from the Epstein-Barr virus,

bnrf1HV

the BNRF1 gene from the herpes virus.

Usage

data(bnrf1)

Format

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

Author

Martin Maechler (original packaging for R).

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")
# \dontshow{
 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)