add_sample_annotation: Add sample annotation to Skyline data frame

In ahmohamed/lipidr: Data Mining and Analysis of Lipidomics Datasets

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, ]

ahmohamed/lipidr documentation built on Aug. 17, 2022, 1:35 a.m.