Description References Examples
This dataset is a list containing the following components:
dna
: a DNAbin object alignment of FASTA sequences obtained
by cloning and Sanger sequencing (sequenceID, nucleotide
sequence); sequence labels contain sequence identifiers,
individual IDs, and dates, separated by "_".
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.
records
: a list of dataframes containing information about
the dates of first and last vaccinations, and shedding data
(viral copy number) for some samples.
dna.info
: an indication of the samples from which the DNA
sequences were obtained.
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 42 43 44 45 46 47 48 | ## Not run:
## LOAD DATA ##
data(HorseFluRaw)
attach(HorseFluRaw)
## EXAMINE CONTENT ##
## individual info
head(individuals)
## records info
lapply(records, head)
## DNA sequences
dna
## CREATE OBKDATA ##
x <- new("obkData", individuals=individuals, records=records,
dna=dna, sampleID=dna.info$sampleID)
## MANIPULATE OBJECT ##
## How many individuals and sequences?
get.nindividuals(x)
get.nsequences(x)
## How many sequences per individual?
ind <- table(get.data(x, "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(x, individualID="42")
get.nsequences(ind.42)
## How many samples?
length(unique(get.data(x, "sampleID", where="dna")))
## How many sequences per sample?
table(get.data(x, "sampleID", where="dna"))
detach(HorseFluRaw)
## End(Not run)
|
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