Commit 85722e65 authored by Jakob Wirbel's avatar Jakob Wirbel

re-roxygenized.

parent 7a98226f
......@@ -56,7 +56,7 @@ Imports:
corrplot
License: GPL-3
LazyData: true
RoxygenNote: 6.1.0
RoxygenNote: 6.1.1
biocViews: ImmunoOncology, Metagenomics, Classification, Microbiome,
Sequencing, Preprocessing, Clustering, FeatureExtraction,
GeneticVariability, MultipleComparison,Regression
......
......@@ -32,20 +32,19 @@ of intense research. For this, robust statistical modeling and biomarker
extraction toolkits are crucially needed!
}
\author{
\strong{Maintainer}: Konrad Zych
\email{konrad.zych@embl.de} (0000-0001-7426-0516)
\strong{Maintainer}: Konrad Zych \email{konrad.zych@embl.de} (0000-0001-7426-0516)
Authors:
\itemize{
\item Jakob Wirbel \email{jakob.wirbel@embl.de} (0000-0002-4073-3562)
\item Georg Zeller \email{zeller@embl.de} (0000-0003-1429-7485)
\item Jakob Wirbel \email{jakob.wirbel@embl.de} (0000-0002-4073-3562)
\item Georg Zeller \email{zeller@embl.de} (0000-0003-1429-7485)
}
Other contributors:
\itemize{
\item Morgan Essex \email{morgan.essex@embl.de} [contributor]
\item Nicolai Karcher [contributor]
\item Kersten Breuer [contributor]
\item Morgan Essex \email{morgan.essex@embl.de} [contributor]
\item Nicolai Karcher [contributor]
\item Kersten Breuer [contributor]
}
}
......@@ -6,7 +6,7 @@
\usage{
normalize.features(siamcat,
norm.method = c("rank.unit", "rank.std",
"log.std", "log.unit", "log.clr"),
"log.std", "log.unit", "log.clr", "pass"),
norm.param = list(log.n0 = 1e-06, sd.min.q = 0.1,
n.p = 2, norm.margin = 1),
feature.type='filtered',
......@@ -16,7 +16,8 @@ normalize.features(siamcat,
\item{siamcat}{an object of class \link{siamcat-class}}
\item{norm.method}{string, normalization method, can be one of these:
'\code{c('rank.unit', 'rank.std', 'log.std', 'log.unit', 'log.clr')}}
'\code{c('rank.unit', 'rank.std', 'log.std', 'log.unit', 'log.clr',
'pass')}}
\item{norm.param}{list, specifying the parameters of the different
normalization methods, see details for more information}
......@@ -39,7 +40,7 @@ This function performs feature normalization according to user-
specified parameters.
}
\details{
There are five different normalization methods available:
There are six different normalization methods available:
\itemize{
\item \code{'rank.unit'} - converts features to ranks and normalizes
each column (=sample) by the square root of the sum of ranks
......@@ -50,8 +51,9 @@ There are five different normalization methods available:
\item \code{'log.std'} - log-transforms features (after addition of
pseudocounts) and applies z-score standardization
\item \code{'log.unit'} - log-transforms features (after addition of
pseudocounts) and normalizes by features or samples with different
norms}
pseudocounts) and normalizes by features or samples with different norms
\item \code{'pass'} - pass-through normalization will not change the
features}
The list entries in \code{'norm.param'} specify the normalzation parameters,
which are dependant on the normalization method of choice:
......
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