The goal of metaboprep is to:
- Read in and processes (un)targeted metabolite data, saving datasets in tab-delimited format for use elsewhere
- Provide useful summary data in the form of tab-delimited text file and a html report.
- Perform data filtering on the data set using a standard pipeline and according to user-defined thresholds.
Installation
You can install the development version of metaboprep from GitHub with:
# install.packages("pak")
pak::pak("MRCIEU/metaboprep")
Example
This is a basic example which shows you how to load data and run the metaboprep quality control pipeline.
library(metaboprep)
# the data
data_file <- system.file("extdata", "metabolon_v1_example.xlsx", package = "metaboprep")
# import data
dat <- read_metabolon_v1(system.file("extdata", "metabolon_v1_example.xlsx", package = "metaboprep"))
# create the object
m <- Metaboprep(data = dat$data[,,1], samples = dat$samples, features = dat$features)
# run QC
m <- m |>
quality_control(source_layer = "input",
sample_missingness = 0.5,
feature_missingness = 0.3,
total_peak_area_sd = 5,
outlier_udist = 5,
outlier_treatment = "leave_be",
winsorize_quantile = 1.0,
tree_cut_height = 0.5,
pc_outlier_sd = 5,
sample_ids = NULL,
feature_ids = NULL)
#>
#> ── Starting Metabolite QC Process ──────────────────────────────────────────────
#> ℹ Validating input parameters✔ Validating input parameters [4ms]
#> ℹ Sample & Feature Summary Statistics for raw data✔ Sample & Feature Summary Statistics for raw data [541ms]
#> ℹ Copying input data to new 'qc' data layer✔ Copying input data to new 'qc' data layer [12ms]
#> ℹ Assessing for extreme sample missingness >=80% - excluding 0 sample(s)✔ Assessing for extreme sample missingness >=80% - excluding 0 sample(s) [8ms]
#> ℹ Assessing for extreme feature missingness >=80% - excluding 0 feature(s)✔ Assessing for extreme feature missingness >=80% - excluding 0 feature(s) [8ms]
#> ℹ Assessing for sample missingness at specified level of >=50% - excluding 0 sa…✔ Assessing for sample missingness at specified level of >=50% - excluding 0 sa…
#> ℹ Assessing for feature missingness at specified level of >=30% - excluding 0 f…✔ Assessing for feature missingness at specified level of >=30% - excluding 0 f…
#> ℹ Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…✔ Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…
#> ℹ Running sample data PCA outlier analysis at +/- 5 Sdev✔ Running sample data PCA outlier analysis at +/- 5 Sdev [9ms]
#> ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…✔ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#> ℹ Creating final QC dataset...✔ Creating final QC dataset... [526ms]
#> ℹ Metabolite QC Process Completed✔ Metabolite QC Process Completed [7ms]
# view
m
#> <metaboprep::Metaboprep>
#> @ data : num [1:100, 1:100, 1:2] 11.03 10.8 11.47 10.45 9.24 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> .. ..$ : chr [1:100] "comp_id_123" "comp_id_124" "comp_id_125" "comp_id_126" ...
#> .. ..$ : chr [1:2] "input" "qc"
#> .. - attr(*, "qc_sample_missingness")= num 0.5
#> .. - attr(*, "qc_feature_missingness")= num 0.3
#> .. - attr(*, "qc_total_peak_area_sd")= num 5
#> .. - attr(*, "qc_outlier_udist")= num 5
#> .. - attr(*, "qc_outlier_treatment")= chr "leave_be"
#> .. - attr(*, "qc_winsorize_quantile")= num 1
#> .. - attr(*, "qc_tree_cut_height")= num 0.5
#> .. - attr(*, "qc_pc_outlier_sd")= num 5
#> .. - attr(*, "qc_features_exclude_but_keep")= chr(0)
#> @ samples :'data.frame': 100 obs. of 8 variables:
#> .. $ sample_id : chr "ind1" "ind2" "ind3" "ind4" ...
#> .. $ neg : chr "batch1" "batch1" "batch1" "batch1" ...
#> .. $ pos : chr "batch1" "batch1" "batch1" "batch1" ...
#> .. $ run_day : chr "day1" "day1" "day1" "day1" ...
#> .. $ box_id : chr "box1" "box1" "box1" "box1" ...
#> .. $ lot : chr "lot250" "lot250" "lot250" "lot250" ...
#> .. $ reason_excluded: chr NA NA NA NA ...
#> .. $ excluded : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
#> @ features :'data.frame': 100 obs. of 9 variables:
#> .. $ feature_id : chr "comp_id_123" "comp_id_124" "comp_id_125" "comp_id_126" ...
#> .. $ metabolite_id : chr "met1" "met2" "met3" "met4" ...
#> .. $ comp_id : chr "123" "124" "125" "126" ...
#> .. $ pathway : chr "neg" "neg" "neg" "neg" ...
#> .. $ platform : chr "xenobiotic" "xenobiotic" "xenobiotic" "lipid" ...
#> .. $ kegg : chr "K100" "K100" "K100" "K200" ...
#> .. $ hmdb : chr "HMDB1" "HMDB2" "HMDB3" "HMDB4" ...
#> .. $ reason_excluded: chr NA NA NA NA ...
#> .. $ excluded : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
#> @ exclusions :List of 2
#> .. $ samples :List of 5
#> .. ..$ user_excluded : chr(0)
#> .. ..$ extreme_sample_missingness : chr(0)
#> .. ..$ user_defined_sample_missingness : chr(0)
#> .. ..$ user_defined_sample_totalpeakarea: chr(0)
#> .. ..$ user_defined_sample_pca_outlier : chr(0)
#> .. $ features:List of 3
#> .. ..$ user_excluded : chr(0)
#> .. ..$ extreme_feature_missingness : chr(0)
#> .. ..$ user_defined_feature_missingness: chr(0)
#> @ feature_summary: num [1:20, 1:100, 1:2] 0 0 100 12.36 4.25 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:20] "missingness" "outlier_count" "n" "mean" ...
#> .. ..$ : chr [1:100] "comp_id_123" "comp_id_124" "comp_id_125" "comp_id_126" ...
#> .. ..$ : chr [1:2] "input" "qc"
#> .. - attr(*, "qc_tree")=List of 7
#> .. ..$ merge : int [1:97, 1:2] -76 -1 -85 -88 -64 -11 -2 -25 -77 -79 ...
#> .. ..$ height : num [1:97] 0.381 0.387 0.413 0.527 0.528 ...
#> .. ..$ order : int [1:98] 8 25 60 18 22 7 52 19 73 23 ...
#> .. ..$ labels : chr [1:98] "comp_id_123" "comp_id_124" "comp_id_125" "comp_id_126" ...
#> .. ..$ method : chr "complete"
#> .. ..$ call : language stats::hclust(d = dist_matrix, method = "complete")
#> .. ..$ dist.method: NULL
#> .. ..- attr(*, "class")= chr "hclust"
#> .. - attr(*, "qc_outlier_udist")= num 5
#> .. - attr(*, "qc_tree_cut_height")= num 0.5
#> @ sample_summary : num [1:100, 1:20, 1:2] 0.2 0.12 0.16 0 0.01 0.01 0 0.01 0 0 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> .. ..$ : chr [1:20] "missingness" "tpa_total" "tpa_complete_features" "outlier_count" ...
#> .. ..$ : chr [1:2] "input" "qc"
#> .. - attr(*, "qc_varexp")= Named num [1:95] 0.1001 0.0496 0.0448 0.0412 0.0388 ...
#> .. ..- attr(*, "names")= chr [1:95] "PC1" "PC2" "PC3" "PC4" ...
#> .. - attr(*, "qc_num_pcs_scree")= num 2
#> .. - attr(*, "qc_num_pcs_parallel")= int 14
#> .. - attr(*, "qc_outlier_udist")= num 5
# view tree
tree <- attr(m@feature_summary, "qc_tree")
dend <- stats::as.dendrogram(tree)
plot(dend)