Description References Examples
This dataset is an obkData
object with the following components:
individuals
: a dataframe which contains all static
information relating to a horse (individualID), training yard the
horse belongs to (yardID), date of birth, sex, latitude,
longitude.
dna
: an obkSequences object containing DNA
sequences and their meta-information.
records
: a list of dataframes containing information about
the dates of first and last vaccinations, and shedding data
(viral copy number) for some samples.
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, et al. (2012) Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks. PLoS Pathog 8(12): e1003081. doi:10.1371/journal.ppat.1003081
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | ## Not run:
## LOAD DATA ##
data(HorseFlu)
## EXAMINE CONTENT ##
summary(HorseFlu)
## individual info
head(HorseFlu@individuals)
## DNA sequences
HorseFlu@dna
## records info
lapply(HorseFlu@records, head)
## How many individuals and sequences?
get.nindividuals(HorseFlu)
get.nsequences(HorseFlu)
## How many sequences per individual?
ind <- table(get.data(HorseFlu, "individualID", where="dna"))
ind
barplot(sort(ind), horiz=TRUE, las=1,
xlab="number of samples", cex.names=.8)
## How many sequences for this individual?
ind.42 <- subset(HorseFlu, individualID="42")
get.nsequences(ind.42)
## How many samples?
length(unique(get.data(HorseFlu, "sampleID", where="dna")))
## How many sequences per sample?
table(get.data(HorseFlu, "sampleID", where="dna"))
## End(Not run)
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