Import Metabolon Metabolomic Data
metabolon.RmdMetabolon data is…
Import Metabolon data
library(metaboprep)
# example file
filepath <- system.file("extdata", "metabolon_v1.2_example.xlsx", package = "metaboprep")
# import
dat <- read_metabolon(filepath, sheet = 'OrigScale')
# view structure
str(dat)
#> List of 3
#> $ data : num [1:100, 1:104] 98551 43695 44899 37811 36825 ...
#> ..- attr(*, "dimnames")=List of 2
#> .. ..$ : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> .. ..$ : chr [1:104] "123" "124" "125" "126" ...
#> $ samples :'data.frame': 100 obs. of 5 variables:
#> ..$ sample_id : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> ..$ parent_sample_id : chr [1:100] "ps_id" "ps_id" "ps_id" "ps_id" ...
#> ..$ client_identifier: chr [1:100] "FR01234" "FR01235" "FR01236" "FR01237" ...
#> ..$ pair : chr [1:100] "99999" "99999" "99999" "99999" ...
#> ..$ volume_extracted : chr [1:100] "100" "100" "100" "100" ...
#> $ features:'data.frame': 104 obs. of 13 variables:
#> ..$ feature_id : chr [1:104] "123" "124" "125" "126" ...
#> ..$ pathway_sortorder: chr [1:104] "1" "2" "3" "4" ...
#> ..$ biochemical : chr [1:104] "(N(1) + N(8))-acetylspermidine" "1,2,3-benzenetriol sulfate (2)" "1,2-dilinoleoyl-GPC (18:2/18:2)" "1,2-dilinoleoyl-GPE (18:2/18:2)*" ...
#> ..$ super_pathway : chr [1:104] "Amino Acid" "Xenobiotics" "Lipid" "Lipid" ...
#> ..$ sub_pathway : chr [1:104] "Polyamine Metabolism" "Chemical" "Phosphatidylcholine (PC)" "Phosphatidylethanolamine (PE)" ...
#> ..$ platform : chr [1:104] "LC/MS Pos Early" "LC/MS Neg" "LC/MS Pos Late" "LC/MS Pos Late" ...
#> ..$ chemical_id : chr [1:104] "1111" "1112" "1113" "1114" ...
#> ..$ ri : chr [1:104] "2221" "2222" "2223" "2224" ...
#> ..$ mass : chr [1:104] "111.111" "111.11199999999999" "111.113" "111.114" ...
#> ..$ cas : chr [1:104] NA NA "111-11-1" NA ...
#> ..$ pubchem : chr [1:104] NA NA "11111" "11112" ...
#> ..$ kegg : chr [1:104] NA NA NA NA ...
#> ..$ group_hmdb : chr [1:104] NA NA "HMDB123" "HMDB124" ...Create Metaboprep object
Once imported, we pass the data to the Metaboprep class
object.
m <- Metaboprep(data = dat$data,
features = dat$features,
samples = dat$samples)
# view
m
#> <metaboprep::Metaboprep>
#> @ data : num [1:100, 1:104, 1] 98551 43695 44899 37811 36825 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> .. ..$ : chr [1:104] "123" "124" "125" "126" ...
#> .. ..$ : chr "input"
#> @ samples :'data.frame': 100 obs. of 5 variables:
#> .. $ sample_id : chr "ind1" "ind2" "ind3" "ind4" ...
#> .. $ parent_sample_id : chr "ps_id" "ps_id" "ps_id" "ps_id" ...
#> .. $ client_identifier: chr "FR01234" "FR01235" "FR01236" "FR01237" ...
#> .. $ pair : chr "99999" "99999" "99999" "99999" ...
#> .. $ volume_extracted : chr "100" "100" "100" "100" ...
#> @ features :'data.frame': 104 obs. of 13 variables:
#> .. $ feature_id : chr "123" "124" "125" "126" ...
#> .. $ pathway_sortorder: chr "1" "2" "3" "4" ...
#> .. $ biochemical : chr "(N(1) + N(8))-acetylspermidine" "1,2,3-benzenetriol sulfate (2)" "1,2-dilinoleoyl-GPC (18:2/18:2)" "1,2-dilinoleoyl-GPE (18:2/18:2)*" ...
#> .. $ super_pathway : chr "Amino Acid" "Xenobiotics" "Lipid" "Lipid" ...
#> .. $ sub_pathway : chr "Polyamine Metabolism" "Chemical" "Phosphatidylcholine (PC)" "Phosphatidylethanolamine (PE)" ...
#> .. $ platform : chr "LC/MS Pos Early" "LC/MS Neg" "LC/MS Pos Late" "LC/MS Pos Late" ...
#> .. $ chemical_id : chr "1111" "1112" "1113" "1114" ...
#> .. $ ri : chr "2221" "2222" "2223" "2224" ...
#> .. $ mass : chr "111.111" "111.11199999999999" "111.113" "111.114" ...
#> .. $ cas : chr NA NA "111-11-1" NA ...
#> .. $ pubchem : chr NA NA "11111" "11112" ...
#> .. $ kegg : chr NA NA NA NA ...
#> .. $ group_hmdb : chr NA NA "HMDB123" "HMDB124" ...
#> @ 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[0 , 0 , 0 ]
#> @ sample_summary : num[0 , 0 , 0 ]QC Metabolon
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)
#>
#> ── Starting Metabolite QC Process ──────────────────────────────────────────────
#> ℹ Validating input parameters
#> ✔ Validating input parameters [7ms]
#>
#> ℹ Sample & Feature Summary Statistics for raw data
#> ✔ Sample & Feature Summary Statistics for raw data [1.1s]
#>
#> ℹ Copying input data to new 'qc' data layer
#> ✔ Copying input data to new 'qc' data layer [24ms]
#>
#> ℹ Assessing for extreme sample missingness >=80% - excluding 0 sample(s)
#> ✔ Assessing for extreme sample missingness >=80% - excluding 1 sample(s) [16ms]
#>
#> ℹ Assessing for extreme feature missingness >=80% - excluding 0 feature(s)
#> ✔ Assessing for extreme feature missingness >=80% - excluding 0 feature(s) [21m…
#>
#> 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 1 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 [17ms]
#>
#> ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#> [1] 2
#> [1] 99 10
#> ✔ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#>
#> ℹ Creating final QC dataset...
#> ✔ Creating final QC dataset... [1s]
#>
#> ℹ Metabolite QC Process Completed
#> ✔ Metabolite QC Process Completed [20ms]
#>
# view
m
#> <metaboprep::Metaboprep>
#> @ data : num [1:100, 1:104, 1:2] 98551 43695 44899 37811 36825 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:100] "ind1" "ind2" "ind3" "ind4" ...
#> .. ..$ : chr [1:104] "123" "124" "125" "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 7 variables:
#> .. $ sample_id : chr "ind1" "ind2" "ind3" "ind4" ...
#> .. $ parent_sample_id : chr "ps_id" "ps_id" "ps_id" "ps_id" ...
#> .. $ client_identifier: chr "FR01234" "FR01235" "FR01236" "FR01237" ...
#> .. $ pair : chr "99999" "99999" "99999" "99999" ...
#> .. $ volume_extracted : chr "100" "100" "100" "100" ...
#> .. $ reason_excluded : chr NA NA NA NA ...
#> .. $ excluded : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
#> @ features :'data.frame': 104 obs. of 15 variables:
#> .. $ feature_id : chr "123" "124" "125" "126" ...
#> .. $ pathway_sortorder: chr "1" "2" "3" "4" ...
#> .. $ biochemical : chr "(N(1) + N(8))-acetylspermidine" "1,2,3-benzenetriol sulfate (2)" "1,2-dilinoleoyl-GPC (18:2/18:2)" "1,2-dilinoleoyl-GPE (18:2/18:2)*" ...
#> .. $ super_pathway : chr "Amino Acid" "Xenobiotics" "Lipid" "Lipid" ...
#> .. $ sub_pathway : chr "Polyamine Metabolism" "Chemical" "Phosphatidylcholine (PC)" "Phosphatidylethanolamine (PE)" ...
#> .. $ platform : chr "LC/MS Pos Early" "LC/MS Neg" "LC/MS Pos Late" "LC/MS Pos Late" ...
#> .. $ chemical_id : chr "1111" "1112" "1113" "1114" ...
#> .. $ ri : chr "2221" "2222" "2223" "2224" ...
#> .. $ mass : chr "111.111" "111.11199999999999" "111.113" "111.114" ...
#> .. $ cas : chr NA NA "111-11-1" NA ...
#> .. $ pubchem : chr NA NA "11111" "11112" ...
#> .. $ kegg : chr NA NA NA NA ...
#> .. $ group_hmdb : chr NA NA "HMDB123" "HMDB124" ...
#> .. $ 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 "ind13"
#> .. ..$ 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 "179"
#> @ feature_summary: num [1:20, 1:104, 1:2] 0.01 0 99 52876.67 25579.58 ...
#> .. - attr(*, "dimnames")=List of 3
#> .. ..$ : chr [1:20] "missingness" "outlier_count" "n" "mean" ...
#> .. ..$ : chr [1:104] "123" "124" "125" "126" ...
#> .. ..$ : chr [1:2] "input" "qc"
#> .. - attr(*, "qc_tree")=List of 7
#> .. ..$ merge : int [1:102, 1:2] -35 -22 -70 -5 -23 -19 -91 -1 -10 -46 ...
#> .. ..$ height : num [1:102] 0.632 0.646 0.659 0.664 0.671 ...
#> .. ..$ order : int [1:103] 94 100 10 31 17 29 74 89 28 96 ...
#> .. ..$ labels : chr [1:103] "123" "124" "125" "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] 0.00962 0.00962 0.00962 0.00962 0.05769 ...
#> .. - 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 [1:99] 0.0372 0.035 0.0334 0.0327 0.0316 ...
#> .. ..- attr(*, "names")= chr [1:99] "PC1" "PC2" "PC3" "PC4" ...
#> .. - attr(*, "qc_num_pcs_scree")= num 2
#> .. - attr(*, "qc_num_pcs_parallel")= int 16
#> .. - attr(*, "qc_outlier_udist")= num 5