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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.
test.sample.content.normalization <- function(date.input = '2011-11-04', date.checked.output = '2011-11-04'){
# data directories
path.to.input.files <- '../NanoStringNorm/extdata/input/';
path.to.output.files <- '../NanoStringNorm/extdata/output/';
# read input files
x <- read.table(paste(path.to.input.files, 'mRNA_TCDD_matrix.txt', sep = ''), sep = '\t', header = TRUE, as.is = TRUE);
anno <- read.table(paste(path.to.input.files, 'mRNA_TCDD_anno.txt', sep = ''), sep = '\t', header = TRUE, as.is = TRUE);
trait <- read.table(paste(path.to.input.files, 'mRNA_TCDD_strain_info.txt', sep = ''), sep = '\t', header = TRUE, as.is = TRUE);
# read *checked output*
checked.output.hk.sum <- dget(file = gzfile(paste(path.to.output.files, 'mRNA_TCDD_housekeeping.sum_SampleContent_Normalization.txt.gz', sep = '')));
checked.output.hk.geo.mean <- dget(file = gzfile(paste(path.to.output.files, 'mRNA_TCDD_housekeeping.geomean_SampleContent_Normalization.txt.gz', sep = '')));
checked.output.top.geo.mean <- dget(file = gzfile(paste(path.to.output.files, 'mRNA_TCDD_top.geo.mean_SampleContent_Normalization.txt.gz', sep = '')));
checked.output.top.mean <- dget(file = gzfile(paste(path.to.output.files, 'mRNA_TCDD_top.mean_SampleContent_Normalization.txt.gz', sep = '')));
checked.output.total.sum <- dget(file = gzfile(paste(path.to.output.files, 'mRNA_TCDD_total.sum_SampleContent_Normalization.txt.gz', sep = '')));
# run function to get *test output*
test.output.hk.sum <- NanoStringNorm:::sample.content.normalization(x, anno, 'housekeeping.sum', verbose = FALSE);
test.output.hk.geo.mean <- NanoStringNorm:::sample.content.normalization(x, anno, 'housekeeping.geo.mean', verbose = FALSE);
test.output.top.geo.mean <- NanoStringNorm:::sample.content.normalization(x, anno, 'top.geo.mean', verbose = FALSE);
test.output.top.mean <- NanoStringNorm:::sample.content.normalization(x, anno, 'top.mean', verbose = FALSE);
test.output.total.sum <- NanoStringNorm:::sample.content.normalization(x, anno, 'total.sum', verbose = FALSE);
### check1 - compare checked output == test output
check1.1 <- checkEquals(checked.output.hk.sum, test.output.hk.sum);
check1.2 <- checkEquals(checked.output.hk.geo.mean, test.output.hk.geo.mean);
check1.3 <- checkEquals(checked.output.top.geo.mean, test.output.top.geo.mean);
check1.4 <- checkEquals(checked.output.top.mean, test.output.top.mean);
check1.5 <- checkEquals(checked.output.total.sum, test.output.total.sum);
### check2 - test bad input
check2.1 <- checkException(NanoStringNorm:::sample.content.normalization(x, anno, 'garbage', verbose = FALSE));
checks <- c(check1.1 = check1.1, check1.2 = check1.2, check1.3 = check1.3, check1.4 = check1.4,check1.5 = check1.5, check2.1 = check2.1);
if (!all(checks)) print(checks[checks == FALSE]);
return(all(checks))
}
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