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Misc changes #9

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Misc changes #9

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92de0ce
add suffix to channelRename() in order to change it if needed
SamGG Nov 27, 2019
52c6bfb
Merge pull request #1 from ismms-himc/master
SamGG Dec 5, 2020
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15 changes: 9 additions & 6 deletions R/channel_rename.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
#' @param ignore.mass Ignore the mass computation (FALSE by default); if TRUE
#' the mass column is assigned <NA>
#' @export
channelRename <- function(path, dup_handling = "message", verbose = TRUE, na.mass.rm = TRUE, ignore.mass = FALSE) {
channelRename <- function(path, dup_handling = "message", verbose = TRUE, na.mass.rm = TRUE, ignore.mass = FALSE, suffix = "renamed") {
filenames <- file.path(path, dir(path, "\\.fcs$"))
if (length(filenames) == 0) stop("could not find any FCS files at given path")

Expand Down Expand Up @@ -52,7 +52,8 @@ channelRename <- function(path, dup_handling = "message", verbose = TRUE, na.mas
renameFcsFileChannels(dest_path,
filenames,
channels,
verbose = verbose)
verbose = verbose,
suffix = suffix)

if (verbose) message("Export done")
} else {
Expand Down Expand Up @@ -166,7 +167,8 @@ renameFcsFileChannels <- function(dest_path,
for (filename in filenames) {
if (verbose) message(paste0("\t", filename))

fcs <- flowCore::read.FCS(filename)
fcs <- flowCore::read.FCS(filename, transformation = FALSE,
min.limit = NULL, truncate_max_range = FALSE)
# Merge file parameters with channel renames.
params <- fcs@parameters@data
params$name[is.na(params$name)] <- ""
Expand All @@ -178,12 +180,13 @@ renameFcsFileChannels <- function(dest_path,
filename <- basename(filename)
if (suffix != "") {
dest_filename <-
file.path(dest_path, paste0(filename, ".", suffix, ".fcs"))
file.path(dest_path, gsub("\\.fcs$", paste0(".", suffix, ".fcs"),
filename, ignore.case = TRUE))
} else {
dest_filename <- file.path(dest_path, filename)
}

# This if clause prevents bug from occuring if the current fcs file already
# This if clause prevents bug from occuring if the current fcs file already
# has appropriate channel names and descriptions.
if (nrow(params) == 0) {
if (verbose) message("\t--> ", dest_filename)
Expand Down Expand Up @@ -223,4 +226,4 @@ renameFcsFileChannels <- function(dest_path,
flowCore::write.FCS(fcs, dest_filename)
}
}
}
}