add_sample_annotation {lipidr} | R Documentation

## Add sample annotation to Skyline data frame

### Description

Add sample annotation to Skyline data frame

### Usage

    add_sample_annotation(data, annot_file)

### Arguments

`data` | LipidomicsExperiment object.
`annot_file` | CSV file or a data.frame with at least 2 columns, sample names & group(s).

### Value

LipidomicsExperiment with sample group information.

### Examples

    datadir <- system.file("extdata", package = "lipidr")

    # all csv files
    filelist <- list.files(datadir, "data.csv", full.names = TRUE)
    d <- read_skyline(filelist)

    # Add clinical info to existing LipidomicsExperiment object
    clinical_file <- system.file("extdata", "clin.csv", package = "lipidr")
    d <- add_sample_annotation(d, clinical_file)
    colData(d)
    d$group

    # Subset samples using clinical information
    # Note we are subsetting columns
    d[, d$group == "QC"]

    # Subset lipids using lipid annotation
    # Note we are subsetting rows
    d[rowData(d)$istd, ]

[Package lipidr version 2.0.0 Index]