Add sample annotation to Skyline data frame
add_sample_annotation(data, annot_file)LipidomicsExperiment object.
CSV file or a data.frame with at least 2 columns, sample names & group(s).
LipidomicsExperiment with sample group information.
datadir <- system.file("extdata", package = "lipidr")
# all csv files
filelist <- list.files(datadir, "data.csv", full.names = TRUE)
d <- read_skyline(filelist)
#> Successfully read 3 methods.
#> Your data contain 58 samples, 10 lipid classes, 277 lipid molecules.
# 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)
#> DataFrame with 58 rows and 3 columns
#> group Diet BileAcid
#> <character> <character> <character>
#> S1A NormalDiet_water Normal water
#> S2A NormalDiet_water Normal water
#> S3A NormalDiet_water Normal water
#> S4A NormalDiet_water Normal water
#> S5A NormalDiet_water Normal water
#> ... ... ... ...
#> TQC_8 QC QC QC
#> TQC_9 QC QC QC
#> TQC_10 QC QC QC
#> TQC_11 QC QC QC
#> TQC_12 QC QC QC
d$group
#> [1] "NormalDiet_water" "NormalDiet_water" "NormalDiet_water" "NormalDiet_water"
#> [5] "NormalDiet_water" "NormalDiet_water" "NormalDiet_water" "NormalDiet_water"
#> [9] "NormalDiet_water" "NormalDiet_water" "NormalDiet_water" "NormalDiet_DCA"
#> [13] "NormalDiet_DCA" "NormalDiet_DCA" "NormalDiet_DCA" "NormalDiet_DCA"
#> [17] "NormalDiet_DCA" "NormalDiet_DCA" "NormalDiet_DCA" "NormalDiet_DCA"
#> [21] "NormalDiet_DCA" "NormalDiet_DCA" "HighFat_water" "HighFat_water"
#> [25] "HighFat_water" "HighFat_water" "HighFat_water" "HighFat_water"
#> [29] "HighFat_water" "HighFat_water" "HighFat_water" "HighFat_water"
#> [33] "HighFat_water" "HighFat_DCA" "HighFat_DCA" "HighFat_DCA"
#> [37] "HighFat_DCA" "HighFat_DCA" "HighFat_DCA" "HighFat_DCA"
#> [41] "HighFat_DCA" "HighFat_DCA" "HighFat_DCA" "HighFat_DCA"
#> [45] "blank" "blank" "QC" "QC"
#> [49] "QC" "QC" "QC" "QC"
#> [53] "QC" "QC" "QC" "QC"
#> [57] "QC" "QC"
# Subset samples using clinical information
# Note we are subsetting columns
d[, d$group == "QC"]
#> class: LipidomicsExperiment
#> dim: 279 12
#> metadata(2): summarized dimnames
#> assays(3): Retention Time Area Background
#> rownames(279): 1 2 ... 278 279
#> rowData names(26): filename Molecule ... total_cs Class
#> colnames(12): TQC_1 TQC_2 ... TQC_11 TQC_12
#> colData names(3): group Diet BileAcid
# Subset lipids using lipid annotation
# Note we are subsetting rows
d[rowData(d)$istd, ]
#> class: LipidomicsExperiment
#> dim: 10 58
#> metadata(2): summarized dimnames
#> assays(3): Retention Time Area Background
#> rownames(10): 62 63 ... 220 279
#> rowData names(26): filename Molecule ... total_cs Class
#> colnames(58): S1A S2A ... TQC_11 TQC_12
#> colData names(3): group Diet BileAcid