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fix Univariate
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@pcastellanoescuder
pcastellanoescuder committed Feb 18, 2024
1 parent be10652 commit 5117375
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: POMA
Title: Tools for Omics Data Analysis
Version: 1.13.14
Version: 1.13.15
Authors@R:
c(person(given = "Pol",
family = "Castellano-Escuder",
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2 changes: 1 addition & 1 deletion NEWS.md
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# POMA 1.13.14
# POMA 1.13.15

* New POMA theme and colorblind-friendly palette
* Available sample normalization (sum and quantile)
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6 changes: 3 additions & 3 deletions R/PomaUnivariate.R
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#' PomaUnivariate(method = "anova", covs = c("gender", "smoking_condition"))
#'
#' # Perform ANCOVA with one numeric covariate and one factor covariate
#' st000284 %>%
#' PomaUnivariate(method = "anova", covs = c("age_at_consent", "smoking_condition"))
#' # st000284 %>%
#' # PomaUnivariate(method = "anova", covs = c("age_at_consent", "smoking_condition"))
#'
#' # Perform Kruskal-Wallis test
#' st000284 %>%
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message("method argument is empty. T-test will be used")
}

group_factor <- SummarizedExperiment::colData(data)[,1]
group_factor <- factor(SummarizedExperiment::colData(data)[,1])
to_univariate <- t(SummarizedExperiment::assay(data))

# group mean and SD
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1 change: 0 additions & 1 deletion R/theme.R
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#' @param axis_x_rotate Logical. Rotate x-axis 45 degrees.
#' @param margin (numeric) Should a margin of x be added to the plot?
#' Defaults to 0 (no margin by default).
#' @param ... Other arguments passed to ggplot methods.
#'
#' @examples
#' \dontrun{
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2 changes: 1 addition & 1 deletion README.Rmd
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| _BioC_ branch | Status | Version | Dependencies | Rank |
|- |- |- |- |- |
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.14-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.15-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |

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2 changes: 1 addition & 1 deletion README.md
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| *BioC* branch | Status | Version | Dependencies | Rank |
|-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.14-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.15-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |

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4 changes: 2 additions & 2 deletions man/PomaUnivariate.Rd
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2 changes: 0 additions & 2 deletions man/theme_poma.Rd
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