#### Fix some bugs in the documentation

sherman5 authored on 30/06/2020 05:53:52
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 ... ... @@ -8,8 +8,7 @@ 8 8  \usage{ 9 9  patternMarkers(object, threshold = "all", lp = NA, axis = 1) 10 10   11 -\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", 12 - lp = NA, axis = 1) 11 +\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA, axis = 1) 13 12  } 14 13  \arguments{ 15 14  \item{object}{an object of type CogapsResult}

#### tidied up notation around pattern markers

Tom Sherman authored on 05/09/2019 18:14:53
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 ... ... @@ -6,10 +6,10 @@ 6 6  \alias{patternMarkers,CogapsResult-method} 7 7  \title{compute pattern markers statistic} 8 8  \usage{ 9 -patternMarkers(object, threshold = "all", lp = NA) 9 +patternMarkers(object, threshold = "all", lp = NA, axis = 1) 10 10   11 11  \S4method{patternMarkers}{CogapsResult}(object, threshold = "all", 12 - lp = NA) 12 + lp = NA, axis = 1) 13 13  } 14 14  \arguments{ 15 15  \item{object}{an object of type CogapsResult} ... ... @@ -20,6 +20,9 @@ by the first gene to have a lower ranking, i.e. better fit to, a pattern.} 20 20   21 21  \item{lp}{a vector of weights for each pattern to be used for finding 22 22  markers. If NA markers for each pattern of the A matrix will be used.} 23 + 24 +\item{axis}{either 1 or 2, specifying if pattern markers should be calculated using 25 +the rows of the data (1) or the columns of the data (2)} 23 26  } 24 27  \value{ 25 28  By default a non-overlapping list of genes associated with each

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.} 23 23  } 24 24  \value{ 25 25  By default a non-overlapping list of genes associated with each 26 -\code{lp}. If \code{full=TRUE} a data.frame of genes rankings with a column 27 -for each \code{lp} will also be returned. 26 +\code{lp}. 28 27  } 29 28  \description{ 30 29  calculate the most associated pattern for each gene 31 30  } 31 +\examples{ 32 +data(GIST) 33 +pm <- patternMarkers(GIST.result) 34 +}

#### updated config to commit file permissions

Tom Sherman authored on 29/10/2018 19:56:14
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 1 1 old mode 100644 2 2 new mode 100755

#### clean up output

Tom Sherman authored on 02/08/2018 16:52:31
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 ... ... @@ -6,9 +6,10 @@ 6 6  \alias{patternMarkers,CogapsResult-method} 7 7  \title{compute pattern markers statistic} 8 8  \usage{ 9 -patternMarkers(object, threshold = "all", lp = NA, full = FALSE) 9 +patternMarkers(object, threshold = "all", lp = NA) 10 10   11 -\S4method{patternMarkers}{CogapsResult}(object, threshold, lp) 11 +\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", 12 + lp = NA) 12 13  } 13 14  \arguments{ 14 15  \item{object}{an object of type CogapsResult}

#### tests passing

Tom Sherman authored on 31/07/2018 18:45:03
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 ... ... @@ -4,7 +4,6 @@ 4 4  \name{patternMarkers} 5 5  \alias{patternMarkers} 6 6  \alias{patternMarkers,CogapsResult-method} 7 -\alias{patternMarkers} 8 7  \title{compute pattern markers statistic} 9 8  \usage{ 10 9  patternMarkers(object, threshold = "all", lp = NA, full = FALSE)

#### docs

Tom Sherman authored on 26/07/2018 19:21:36
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 ... ... @@ -1,15 +1,15 @@ 1 1  % Generated by roxygen2: do not edit by hand 2 -% Please edit documentation in R/class-CogapsResult.R 2 +% Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R 3 3  \docType{methods} 4 4  \name{patternMarkers} 5 5  \alias{patternMarkers} 6 6  \alias{patternMarkers,CogapsResult-method} 7 +\alias{patternMarkers} 7 8  \title{compute pattern markers statistic} 8 9  \usage{ 9 10  patternMarkers(object, threshold = "all", lp = NA, full = FALSE) 10 11   11 -\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA, 12 - full = FALSE) 12 +\S4method{patternMarkers}{CogapsResult}(object, threshold, lp) 13 13  } 14 14  \arguments{ 15 15  \item{object}{an object of type CogapsResult} ... ... @@ -20,9 +20,6 @@ by the first gene to have a lower ranking, i.e. better fit to, a pattern.} 20 20   21 21  \item{lp}{a vector of weights for each pattern to be used for finding 22 22  markers. If NA markers for each pattern of the A matrix will be used.} 23 - 24 -\item{full}{logical indicating whether to return the ranks of each gene for 25 -each pattern} 26 23  } 27 24  \value{ 28 25  By default a non-overlapping list of genes associated with each ... ... @@ -32,4 +29,3 @@ for each \code{lp} will also be returned. 32 29  \description{ 33 30  calculate the most associated pattern for each gene 34 31  } 35 -

#### cleaned up directory

Tom Sherman authored on 26/07/2018 18:15:21
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 1 1 new file mode 100644 ... ... @@ -0,0 +1,35 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/class-CogapsResult.R 3 +\docType{methods} 4 +\name{patternMarkers} 5 +\alias{patternMarkers} 6 +\alias{patternMarkers,CogapsResult-method} 7 +\title{compute pattern markers statistic} 8 +\usage{ 9 +patternMarkers(object, threshold = "all", lp = NA, full = FALSE) 10 + 11 +\S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA, 12 + full = FALSE) 13 +} 14 +\arguments{ 15 +\item{object}{an object of type CogapsResult} 16 + 17 +\item{threshold}{the type of threshold to be used. The default "all" will 18 +distribute genes into pattern with the lowest ranking. The "cut" thresholds 19 +by the first gene to have a lower ranking, i.e. better fit to, a pattern.} 20 + 21 +\item{lp}{a vector of weights for each pattern to be used for finding 22 +markers. If NA markers for each pattern of the A matrix will be used.} 23 + 24 +\item{full}{logical indicating whether to return the ranks of each gene for 25 +each pattern} 26 +} 27 +\value{ 28 +By default a non-overlapping list of genes associated with each 29 +\code{lp}. If \code{full=TRUE} a data.frame of genes rankings with a column 30 +for each \code{lp} will also be returned. 31 +} 32 +\description{ 33 +calculate the most associated pattern for each gene 34 +} 35 +