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Fix some bugs in the documentation

sherman5 authored on 30/06/2020 05:53:52
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@@ -8,8 +8,7 @@
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 \usage{
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 patternMarkers(object, threshold = "all", lp = NA, axis = 1)
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-\S4method{patternMarkers}{CogapsResult}(object, threshold = "all",
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-  lp = NA, axis = 1)
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+\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA, axis = 1)
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 }
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 \arguments{
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 \item{object}{an object of type CogapsResult}
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tidied up notation around pattern markers

Tom Sherman authored on 05/09/2019 18:14:53
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@@ -6,10 +6,10 @@
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 \alias{patternMarkers,CogapsResult-method}
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 \title{compute pattern markers statistic}
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 \usage{
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-patternMarkers(object, threshold = "all", lp = NA)
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+patternMarkers(object, threshold = "all", lp = NA, axis = 1)
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 \S4method{patternMarkers}{CogapsResult}(object, threshold = "all",
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-  lp = NA)
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+  lp = NA, axis = 1)
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 }
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 \arguments{
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 \item{object}{an object of type CogapsResult}
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@@ -20,6 +20,9 @@ by the first gene to have a lower ranking, i.e. better fit to, a pattern.}
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 \item{lp}{a vector of weights for each pattern to be used for finding
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 markers. If NA markers for each pattern of the A matrix will be used.}
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+
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+\item{axis}{either 1 or 2, specifying if pattern markers should be calculated using
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+the rows of the data (1) or the columns of the data (2)}
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 }
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 \value{
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 By default a non-overlapping list of genes associated with each
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added amplitudeMarkers function

Tom Sherman authored on 18/06/2019 15:09:16
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@@ -23,9 +23,12 @@ markers. If NA markers for each pattern of the A matrix will be used.}
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 }
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 \value{
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 By default a non-overlapping list of genes associated with each
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-\code{lp}. If \code{full=TRUE} a data.frame of genes rankings with a column
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-for each \code{lp} will also be returned.
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+\code{lp}.
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 }
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 \description{
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 calculate the most associated pattern for each gene
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 }
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+\examples{
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+data(GIST)
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+pm <- patternMarkers(GIST.result)
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+}
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updated config to commit file permissions

Tom Sherman authored on 29/10/2018 19:56:14
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old mode 100644
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new mode 100755
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clean up output

Tom Sherman authored on 02/08/2018 16:52:31
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@@ -6,9 +6,10 @@
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 \alias{patternMarkers,CogapsResult-method}
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 \title{compute pattern markers statistic}
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 \usage{
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-patternMarkers(object, threshold = "all", lp = NA, full = FALSE)
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+patternMarkers(object, threshold = "all", lp = NA)
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-\S4method{patternMarkers}{CogapsResult}(object, threshold, lp)
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+\S4method{patternMarkers}{CogapsResult}(object, threshold = "all",
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+  lp = NA)
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 }
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 \arguments{
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 \item{object}{an object of type CogapsResult}
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tests passing

Tom Sherman authored on 31/07/2018 18:45:03
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@@ -4,7 +4,6 @@
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 \name{patternMarkers}
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 \alias{patternMarkers}
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 \alias{patternMarkers,CogapsResult-method}
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-\alias{patternMarkers}
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 \title{compute pattern markers statistic}
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 \usage{
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 patternMarkers(object, threshold = "all", lp = NA, full = FALSE)
Tom Sherman authored on 26/07/2018 19:21:36
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@@ -1,15 +1,15 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/class-CogapsResult.R
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+% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
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 \name{patternMarkers}
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 \alias{patternMarkers}
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 \alias{patternMarkers,CogapsResult-method}
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+\alias{patternMarkers}
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 \title{compute pattern markers statistic}
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 \usage{
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 patternMarkers(object, threshold = "all", lp = NA, full = FALSE)
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-\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA,
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-  full = FALSE)
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+\S4method{patternMarkers}{CogapsResult}(object, threshold, lp)
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 }
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 \arguments{
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 \item{object}{an object of type CogapsResult}
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@@ -20,9 +20,6 @@ by the first gene to have a lower ranking, i.e. better fit to, a pattern.}
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 \item{lp}{a vector of weights for each pattern to be used for finding
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 markers. If NA markers for each pattern of the A matrix will be used.}
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-
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-\item{full}{logical indicating whether to return the ranks of each gene for
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-each pattern}
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 }
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 \value{
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 By default a non-overlapping list of genes associated with each
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@@ -32,4 +29,3 @@ for each \code{lp} will also be returned.
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 \description{
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 calculate the most associated pattern for each gene
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 }
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-
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cleaned up directory

Tom Sherman authored on 26/07/2018 18:15:21
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new file mode 100644
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@@ -0,0 +1,35 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/class-CogapsResult.R
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+\docType{methods}
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+\name{patternMarkers}
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+\alias{patternMarkers}
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+\alias{patternMarkers,CogapsResult-method}
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+\title{compute pattern markers statistic}
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+\usage{
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+patternMarkers(object, threshold = "all", lp = NA, full = FALSE)
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+
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+\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA,
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+  full = FALSE)
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+}
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+\arguments{
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+\item{object}{an object of type CogapsResult}
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+
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+\item{threshold}{the type of threshold to be used. The default "all" will
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+distribute genes into pattern with the lowest ranking. The "cut" thresholds
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+by the first gene to have a lower ranking, i.e. better fit to, a pattern.}
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+
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+\item{lp}{a vector of weights for each pattern to be used for finding
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+markers. If NA markers for each pattern of the A matrix will be used.}
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+
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+\item{full}{logical indicating whether to return the ranks of each gene for
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+each pattern}
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+}
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+\value{
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+By default a non-overlapping list of genes associated with each
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+\code{lp}. If \code{full=TRUE} a data.frame of genes rankings with a column
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+for each \code{lp} will also be returned.
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+}
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+\description{
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+calculate the most associated pattern for each gene
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+}
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+