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readLxb <- function(paths, filter=TRUE, text=FALSE) {
# Read multiple LXB files and return a list of matrices (one for each LXB).
#
# If 'text=TRUE' then each item is a list with a 'text' and 'data' entry.
# The 'text' is the text segment of the LXB file and the 'data' entry is
# the data segment (same as the matrix return when 'text=FALSE').
#
# If only one LXB is read then the head of the list is returned instead of
# returning a list with only one element.
#
# If 'filter=TRUE' then bad reads are dropped (reads which have no bead ID
# or which did not pass the doublet discriminator test). Otherwise all
# data is included in the output.
#
# The name of each LXB file is used to set the 'names' attribute of the
# returned list. If the name ends with a letter and a 1-2 digit number
# then it is assumed that this encodes the row&column of each well on a
# plate. In this case the output will be sorted by column and the 'names'
# attribute is set to the well name instead of the full file name.
go <- function(filename) {
x <- .Call("read_lxb", as.character(filename), as.logical(text))
if (!is.null(x)) {
if (!is.null(x$data) && filter && 'RID' %in% colnames(x$data)
&& 'DBL' %in% colnames(x$data))
x$data <- x$data[x$data[ ,'RID'] != 0 & x$data[ ,'DBL'] != 0, ]
if (!text)
x <- x$data
}
x
}
names <- Sys.glob(paths)
lxbs <- lapply(names, go)
m <- regexec(".*([a-zA-Z])([0-9]+)[.]lxb", names)
if (all(lapply(m, '[', 1L) != -1)) {
# All names contain row & column information, extract into data frame
parts <- do.call(rbind, lapply(regmatches(names, m), '[', c(2L,3L)))
df <- data.frame(row=parts[ ,1], column=as.integer(parts[ ,2]))
# Order LXBs by: A1, B1, ..., A2, B2, ...
idx <- with(df, order(column, row))
names(lxbs) <- with(df, paste(row, column, sep=""))
lxbs <- lxbs[idx]
} else {
# No row & column information found, use filename
names(lxbs) <- lapply(names, function(x) sub(".lxb", "", basename(x)))
}
if (length(lxbs) == 1)
lxbs <- lxbs[[1]]
lxbs
}
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