OutbreakTools (version 0.1-16)

HorseFluRaw: Raw dataset from the Newmarket 2003 equine influenza outbreak

Description

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.

References

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

Examples

# 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)


# }