Commit 831c189b authored by Jakob Wirbel's avatar Jakob Wirbel
Browse files

new parameter for association checks.

parent 57dbc021
...@@ -9,7 +9,7 @@ check.associations(siamcat, fn.plot=NULL, color.scheme = "RdYlBu", ...@@ -9,7 +9,7 @@ check.associations(siamcat, fn.plot=NULL, color.scheme = "RdYlBu",
detect.lim = 1e-06, pr.cutoff = 1e-6, max.show = 50, detect.lim = 1e-06, pr.cutoff = 1e-6, max.show = 50,
plot.type = "quantile.box", plot.type = "quantile.box",
panels = c("fc","auroc"), prompt = TRUE, panels = c("fc","auroc"), prompt = TRUE,
feature.type = 'filtered', verbose = 1) feature.type = 'filtered', paired=NULL, verbose = 1)
} }
\arguments{ \arguments{
\item{siamcat}{object of class \link{siamcat-class}} \item{siamcat}{object of class \link{siamcat-class}}
...@@ -57,6 +57,9 @@ Please only change this paramter if you know what you are doing! ...@@ -57,6 +57,9 @@ Please only change this paramter if you know what you are doing!
If \code{feature.type} is \code{"normalized"}, the normalized abundances If \code{feature.type} is \code{"normalized"}, the normalized abundances
will not be log10-transformed.} will not be log10-transformed.}
\item{paired}{character, column name of the meta-variable containing
information for a paired test}
\item{verbose}{integer, control output: \code{0} for no output at all, \item{verbose}{integer, control output: \code{0} for no output at all,
\code{1} for only information about progress and success, \code{2} for \code{1} for only information about progress and success, \code{2} for
normal level of information and \code{3} for full debug information, normal level of information and \code{3} for full debug information,
......
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