lipidr for your analysis using numerical matrix as input, you need 2 files:
lipidr can convert these 2 files to
LipidomicsExperiment as follows:
d <- as_lipidomics_experiment(read.csv("data_matrix.csv")) d <- add_sample_annotation(d, "data_clin.csv")
lipidr also requires 2 files:
d <- read_skyline("Skyline_export.csv") d <- add_sample_annotation(d, "data_clin.csv")
lipidr represents lipidomics datasets as a LipidomicsExperiment, which extends SummarizedExperiment, to facilitate integration with other Bioconductor packages.
lipidr generates various plots, such as box plots or PCA, for quality control of samples and measured lipids. Lipids can be filtered by their %CV. Normalization methods with and without internal standards are also supported.
Univariate analysis can be performed using any of the loaded clinical variables, which can be readily visualized as volcano plots. Multi-group comparisons and adjusting for confounding variables is also supported (refer to examples on www.lipidr.org). A novel lipid set enrichment analysis is implemented to detect preferential regulation of certain lipid classes, total chain lengths or unsaturation patterns. Plots for visualization of enrichment results are also implemented.
lipidr implements PCA, PCoA and OPLS(DA) to reveal patterns in data and discover variables related to an outcome of interest. Top associated lipids as well as scores and loadings plots can be interactively investigated using
In R console, type:
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("lipidr")
In R console, type:
You can use
lipidr in a containerized form by pulling the image from docker hub.
docker pull ahmohamed/lipidr docker run -e PASSWORD=bioc -p 8787:8787 ahmohamed/lipidr:latest
In your browser, navigate to RStudio will be available on your web browser at
http://localhost:8787. The USER is fixed to always being
rstudio. The password in the above command is given as
bioc but it can be set to anything. For more information on how-to-use, refer to Bioconductor help page.
You can access your local files by mapping to the container:
docker run -e PASSWORD=bioc -p 8787:8787 \ -v "path/to/data_folder":"/home/rstudio/data_folder" \ ahmohamed/lipidr:latest
You should see
data_folder in your working directory.
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