Add sample annotation to Skyline data frame

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)
#> 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