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useDynLib(samExploreR,.registration = TRUE, .fixes = "C_") | ||
#useDynLib(samExploreR,.registration = TRUE) | ||
import(ggplot2) | ||
exportPattern("^[^\\.]") | ||
export("samExplore") |
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\name{df_intersect} | ||
\alias{df_intersect} | ||
\docType{data} | ||
\title{ | ||
Example data for plotting output of samExplore function. | ||
} | ||
\description{ | ||
Example data for plotting output of samExplore function. | ||
} | ||
\usage{data("df_intersect")} | ||
\format{ | ||
A data frame with 1125 observations on the following 3 variables. | ||
\describe{ | ||
\item{\code{Label}}{a character vector} | ||
\item{\code{Variable}}{a numeric vector} | ||
\item{\code{Value}}{a numeric vector} | ||
} | ||
} | ||
\details{ | ||
is a dataframe object | ||
} | ||
\value{Example data for plotting results.} | ||
\examples{ | ||
data(df_intersect) | ||
|
||
} | ||
\keyword{datasets} |
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\name{df_sole} | ||
\alias{df_sole} | ||
\docType{data} | ||
\title{ | ||
Example data for plotting output of samExplore function. | ||
} | ||
\description{ | ||
|
||
Example data for plotting output of samExplore function. | ||
} | ||
\usage{data("df_sole")} | ||
\format{ | ||
A data frame with 1125 observations on the following 3 variables. | ||
\describe{ | ||
\item{\code{Label}}{a character vector} | ||
\item{\code{Variable}}{a numeric vector} | ||
\item{\code{Value}}{a numeric vector} | ||
} | ||
} | ||
\details{ | ||
is a dataframe object | ||
} | ||
\value{Example data for plotting results.} | ||
\examples{ | ||
data(df_sole) | ||
|
||
} | ||
\keyword{datasets} |
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\name{exploreRep} | ||
\alias{exploreRep} | ||
\title{exploreRep: function to explore the reproducibility} | ||
\description{This function explores the reproducibility of analysis with annotation altering} | ||
\usage{ | ||
exploreRep((df_d, lbl_vect, f)) | ||
} | ||
\arguments{ | ||
\item{df_d}{ a dataframe containing the dataset to explore with 3 columns: | ||
label, f ratio, value to compare (e.g. number of differentially | ||
expressed genes)} | ||
\item{lbl_vect}{a vector of character strings specifing the labels for | ||
which the analysis should be run} | ||
\item{f}{ A numeric value of f for which the analysis should be run} | ||
} | ||
\details{ | ||
\code{exploreRep} function to explore the reproducibility of the analysis | ||
with altering of annotation. It runs ANOVA test for values to compare | ||
(e.g. number of differentially expressed genes) corresponding to different | ||
Annotation labels (i.e. analysis' run for different annotation types) | ||
This function takes as input a dataframe containing the dataset to explore. | ||
Here is the example of the dataframe | ||
\preformatted{ | ||
... | ||
AnnotA 0.1 13 | ||
AnnotB 0.1 101 | ||
AnnotC 0.1 36 | ||
AnnotA 0.1 13 | ||
AnnotB 0.1 101 | ||
AnnotC 0.1 36 | ||
AnnotA 0.4 40 | ||
AnnotB 0.4 153 | ||
AnnotC 0.4 62 | ||
AnnotA 0.8 71 | ||
AnnotB 0.8 203 | ||
AnnotC 0.8 160 | ||
... | ||
} | ||
\code{exploreRob} | ||
Thired column gives the values to compare (here number of differentially | ||
expressed genes). | ||
\code{exploreRep} function subsets the dataset to consider only valyes for one | ||
f and runs ANOVA test for groups corresponding to annotations of interest. | ||
} | ||
\value{ | ||
An output of aov function | ||
} | ||
\author{Alexey Stupnikov and Shailesh Tripathi} | ||
%\note{} | ||
\examples{ | ||
%\dontrun{ | ||
#library(samExploreR) | ||
data("df_sole") | ||
#run ANOVA for annotation types labeled 'New, Gene' and 'New, Exon' and | ||
#f value 0.9 | ||
exploreRep(df_sole, lbl_vect = c('New, Gene', 'Old, Gene'), f = 0.9) | ||
#run ANOVA for annotation type labeled 'Old' and 'New' and f value 0.5 | ||
exploreRep(df_sole, lbl_vect = c('New, Gene', 'Old, Gene'), f = 0.5) | ||
%} | ||
} |
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