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# The NanoStringNorm package is copyright (c) 2012 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.
output.formatting <- function(x, anno, OtherNorm = 'none', round.values = FALSE, is.log = FALSE, take.log = FALSE, verbose = TRUE) {
if ( (!is.logical(round.values) | !is.logical(take.log)) | is.na(round.values) | is.na(take.log) | !is.logical(is.log) | is.na(is.log) ) {
stop('OUTPUT.FORMATTING: Round and take.log and is.log need to be TRUE or FALSE\n\n');
}
if ( is.log == TRUE & take.log == TRUE) {
warning("OUTPUT.FORMATTING: Are you sure you want to take the log of logged data? Both is.log and take.log are TRUE.");
}
# shouldn't be log-transforming z-scores
if (OtherNorm %in% c('rank.normal','zscore') & verbose == TRUE) {
cat('OUTPUT.FORMATTING: log/rounding of zscores/rank.normal is intentionally not implemented.\n\n');
}
# round the data to discrete values.
if (round.values == TRUE) {
x <- round(x, digits = 0);
}
# log2 transformation
if (take.log == TRUE & !OtherNorm %in% c('rank.normal','zscore')) {
# handle negative values
if (any(na.omit(x) < 1)) {
if (verbose) {
cat('log: Setting values less than 1 to 1 in order to calculate the log in positive space.\n\n');
}
# set all values less than one on the raw scale to 0 on the log scale i.e. undetected
x[x < 1] <- 1;
}
# log-transform (base2 by default)
x <- signif(log2(x), 4);
}
return(x);
}
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