Nothing
fread.OTU <- function(file, sep="auto") {
input <- data.table::fread(file, na.strings=c("",".","NA"))
df <- as.data.frame(input)
rownames(df) <- df[,1]
df <- df[, -1]
valid.OTU(df)
df$taxonomy <- as.character(df$taxonomy)
return(df)
}
read.OTU <- function(file, sep=",") {
df <- read.table(file, sep=sep, header=T, row.names=1,
na.strings=c("",".","NA"))
valid.OTU(df)
df$taxonomy <- as.character(df$taxonomy)
return(df)
}
fread.meta <- function(file, sep="auto") {
input <- data.table::fread(file, na.strings=c("",".","NA"))
df <- as.data.frame(input)
rownames(df) <- df[,1]
df <- df[, -1]
return(df)
}
read.meta <- function(file, sep=",") {
input <- read.table(file, header=TRUE, row.names=1, sep=sep,
na.strings=c("",".","NA"))
### PUT META DATA VALIDATION HERE
return(input)
}
write.data <- function(data, file) {
file <- .ensure.filepath(file, "csv")
write.csv(data, file=file, quote=FALSE)
}
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