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# The NanoStringNorm package is copyright (c) 2011 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.
get.sample.summary.stats <- function(x, anno) {
# calculate mean of each sampleContent
sample.mean <- apply(
X = x[grep('Endogenous', anno$Code.Class),],
MARGIN = 2,
FUN = mean,
na.rm = TRUE
);
# calculate SD of each sampleContent
sample.sd <- apply(
X = x[grep('Endogenous', anno$Code.Class),],
MARGIN = 2,
FUN = sd,
na.rm = TRUE
);
# calculate proportion missing values
sample.proportion.missing <- apply(
X = x[grep('Endogenous', anno$Code.Class),],
MARGIN = 2,
FUN = function(y) { sum(y <= 0, na.rm = TRUE) / length(y); }
);
return(
data.frame(
row.names = names(x),
Sample.Mean = sample.mean,
Sample.SD = sample.sd,
Sample.Missing = sample.proportion.missing
)
);
}
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