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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| useDynLib(samExploreR,.registration = TRUE, .fixes = "C_") | ||
| #useDynLib(samExploreR,.registration = TRUE) | ||
| import(ggplot2) | ||
| exportPattern("^[^\\.]") | ||
| export("samExplore") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| \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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