Nothing
#' @rdname read_softmax_template
#' @export
read_softmax5_template <- function(file,
include_unspecified = FALSE,
zeropad_wells = FALSE, #ignored
wellsAsFactors = TRUE,
groupsAsFactors = TRUE,
typesAsFactors = TRUE,
encoding = "guess",
...) {
if (encoding == "guess") {
encoding <- readr::guess_encoding(file)[[1, "encoding"]]
}
d <- utils::read.delim(
file = file,
header = FALSE,
skip = 0,
col.names = c(
"Group",
"Type",
"Sample",
"DescriptionNumber",
"Descriptor1.Units",
"Descriptor1.Name",
"Descriptor1.Value",
"HANGING"
),
blank.lines.skip = FALSE,
#fileEncoding = encoding,
stringsAsFactors = FALSE,
...
)
# Remove the HANGING column and the last row, which contains only "~End"
d <- d[1:96, seq_len(length(d) - 1)]
# Add Well names
x <- expand.grid(Row = LETTERS[1:8], Col = 1:12)
if (zeropad_wells) x$Col <- sprintf("%02d", x$Col)
x$Well <- paste0(x$Row, x$Col)
d$Well <- c(x[order(x$Row), ]$Well)
# Remove unspecified wells
if (include_unspecified == FALSE) {
d <- d[d$Type != "" & !is.na(d$DescriptionNumber), ]
}
softermax.template(
d,
wellsAsFactors = wellsAsFactors,
groupsAsFactors = groupsAsFactors,
typesAsFactors = typesAsFactors
)
}
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