SMITIDstruct (version 0.0.5)

loadViralPop: loadViralPop

Description

Load all ViralPop observated in the file.obs

Usage

loadViralPop(directory, listFiles, listCol = list(id = "id", timeObs =
  "time", filename = "filename"), file.extension = "fasta")

Arguments

directory

path where is data

listFiles

a dataframe with host ID, time observation and file name (filename.fasta)

listCol

a list of listFiles colomns names ("id", "timeObs", "filename")

file.extension

genotype file extension

Value

a vector of VirlaPop object

Examples

# NOT RUN {
path = system.file("extdata", "data-simul/", package="SMITIDstruct")
files <- list.files(path, pattern = ".*.fasta" ,full.names=FALSE)
lfileinfo <- sapply(files,function(x){return(substr(x,1,nchar(x)-6))})
splitFiles <- strsplit(lfileinfo, "_");
listF <- cbind(data.frame(matrix(unlist(splitFiles),nrow=length(splitFiles), byrow=TRUE),
               stringsAsFactors = FALSE), names(splitFiles))
colnames(listF) <- c("id", "time", "filename")
lvpop <- loadViralPop(path,listF)
# }