poplin-class: The poplin class

In jaehyunjoo/poplin: LC/MS Metabolomics Data Processing Utilities

Description

The poplin class is designed to process LC/MS data. It is an extension of the standard SummarizedExperiment class, and supports additional containers for data processing results (e.g., normalization, imputation) via poplin_data_list and dimension reduction results (PCA, PLS-DA) via poplin_reduced_list.

Usage

## Constructor
poplin(..., poplin_data_list = list(), poplin_reduced_list = list())

Arguments

...	Arguments passed to the SummarizedExperiment constructor.
poplin_data_list	A list of matrix-like objects containing data processing results.
poplin_reduced_list	A list of matrix-like objects containing dimension reduction results.

Value

A poplin object

Examples

nsamp <- 10
nfeature <- 200
intensity <- rlnorm(nsamp * nfeature, 10, 1)
m <- matrix(intensity, nrow = nfeature, ncol = nsamp)
rownames(m) <- paste0("F", seq_len(nrow(m)))
colnames(m) <- paste0("S", seq_len(ncol(m)))
poplin(assays = list(raw = m))

## Coercion from an SummarizedExperiment object
se <- SummarizedExperiment(assays = list(raw = m))
as(se, "poplin")

jaehyunjoo/poplin documentation built on Jan. 8, 2022, 1:13 a.m.