formatForAnalysis {ASICS} | R Documentation |
Create an object of class SummarizedExperiment
to use in
functions pca
, oplsda
or
kruskalWallis
.
formatForAnalysis(data, design = NULL, feature_info = NULL, zero.threshold = 100, zero.group = NULL, outliers = NULL)
data |
A data frame containing omics dataset with samples in columns and features of interest in rows (metabolites/buckets...). |
design |
A data frame describing the colums of |
feature_info |
A data frame describing the rows of |
zero.threshold |
Remove features having a proportion of zeros larger
than or equal to |
zero.group |
Variable name of design data frame specifying the group
variable used to remove features with a proportion of zeros larger than or
equal to |
outliers |
Names of the outliers (samples) to remove. |
An object of type SummarizedExperiment
with metabolite
data given as buckets or quantified metabolites.
# Import quantification results if (require("ASICSdata", quietly = TRUE)) { quantif_path <- system.file("extdata", "results_ASICS.txt", package = "ASICSdata") quantification <- read.table(quantif_path, header = TRUE, row.names = 1) # Import design design <- read.table(system.file("extdata", "design_diabete_example.txt", package = "ASICSdata"), header = TRUE) # Create object for analysis and remove features with more than 25% of zeros analysis_obj <- formatForAnalysis(quantification, design = design, zero.threshold = 25, zero.group = "condition") }