Multi-Block PLS Discriminant Analysis
The Multi-Block PLS Discriminant Analysis method
Metabolomics is a powerful phenotyping tool, generating complex data that need dedicated treatments to enrich knowledge of biological systems. In particular, to investigate relations between experimental factors, phenotypes and metabolism, discriminant statistical analyses are generally performed separately on metabolomic datasets, complemented by associations with metadata. Another relevant strategy is to simultaneously analyse thematic data blocks by a multi-block partial least squares discriminant analysis (MBPLSDA) allowing determining the importance of variables of the different data blocks in discriminating groups of observations, taking into account data structure.
References:
Wold, S. (Ed.). (1984). Three PLS algorithms according to SW. In Report from the symposium MULTDAST (multivariate data analysis in science and technology) (pp. 26–30). Umeå, Sweden
Westerhuis, J. A., Kourti, T., & Macgregor, J. F. (1998). Analysis of multi block and hierarchical PCA and PLS models. Journal of Chemometrics, 12, 301–321.
A selection of reduced non-targeted metabolomics datasets from an article of Zhang et al. have been used to illustrate the method application. (Zhang, Y.; Barupal, D.K.; Fan, S.; Gao, B.; Zhu, C.; Flenniken, A.M.; McKerlie, C.; Nutter, L.M.J.; Lloyd, K.C.K.; Fiehn, O. Sexual Dimorphism of the Mouse Plasma Metabolome Is Associated with Phenotypes of 30 Gene Knockout Lines. Metabolites 2023, 13, 947. https://doi.org/10.3390/metabo13080947).
In this study, plasma were analyzed by several metabolomics platforms.
In our example, the 6 samples from 5 mutant groups (Dhfr, Gnpda1, Plk1, Sra1, Ulk3) and the 40 controls were retained, with the exception of 2 animals that had missing values in non-targeted metabolomics. Three HILIC-NEG and 2 HILIC-POS variables were then removed due to missing or infinite values. Lastly, we kept only 2 data blocks (GCTOF and HILIC POS) to reduce the computation time. Always in our example, the objective was to highlight metabolites discriminating males and females.
R environment preparation
#install.packages("knitr")
library(knitr)
opts_chunk$set(echo = TRUE)
# To ensure reproducibility
set.seed(12)Data preprocessing
A demonstration dataset used for this example is imported. It contains 2 metabolomics datasets and 1 sample metadata block, with the groups to be discriminated.
All data blocks should have exactly the same samples (rows). The block dimension can be checked with the following command:
# Check dimension
BlockNames <- names(Zhang2023)
nbrBlocs <- length(BlockNames)
dims <- lapply(X=Zhang2023[BlockNames], FUN=dim)
names(dims) <- BlockNames
dims## $CHSNEG
## [1] 68 163
##
## $CHSPOS
## [1] 68 288
##
## $GCTOF
## [1] 68 108
##
## $HILICPOS
## [1] 68 133
##
## $HILICNEG
## [1] 68 44
##
## $metadata
## [1] 68 2The identical order of samples in the three blocks should be ensured.
# Check rows names in any order
row_names <- lapply(X=Zhang2023[BlockNames], FUN=rownames)
rns <- do.call(cbind, row_names)
rns.unique <- apply(rns, 1, function(x) length(unique(x)))
if (max(rns.unique) > 1) {
stop("Rows names are not identical between blocks.")
}
# Check order of samples
check_row_names <- all(sapply(X=row_names, FUN=identical, y = row_names[[1]]))
if (!check_row_names && max(rns.unique) == 1) {
print("Rows names are not in the same order for all blocks.")
}
# Remove unuseful object for the next steps
rm(row_names, rns, rns.unique, check_row_names)Data visualization by PCA on separate data blocks
PCA on different datablocks is necessary to verify that there is no outlier, and that the data scaling is suited. In our example, unit variance scaling is suited: For both metabolomic dataset, the scatterplot of loadings is homogeneous, and there are no outliers. With other datasets, particularly those containing more noise, it would have been necessary to apply a log transformation with Pareto scaling.
# GCTOF with unit variance scaling
pcaGCTOF <- pcanipalsna(X = scale(GCTOF[,1:dim(GCTOF)[2]]), nlv = nrow(GCTOF),
gs = TRUE,
tol = .Machine$double.eps^0.5, maxit = 200)
## diagram of explained variance
barplot(summary(pcaGCTOF,X = scale(GCTOF[,1:dim(GCTOF)[2]]))$explvar$pvar * 100, names.arg = 1:nrow(GCTOF), main = "diagram of explained variance - PCA GCTOF")
## score plot
plotxy(X= pcaGCTOF$T, group = sample_metadata$Gender,
asp = 0, col = 3:4, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = FALSE,
legend = TRUE, main = "components - PCA GCTOF", ncol = 1,
pch=16)
## loading plot
plotxy(X= pcaGCTOF$P, group = NULL,
asp = 0, col = NULL, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = TRUE,
legend = FALSE, main = "loadings - PCA GCTOF", ncol = 1,
cex=0.8) 
#HILICPOS with unit variance scaling
pcaHILICPOS <- pcanipalsna(X = scale(HILICPOS[,1:dim(HILICPOS)[2]]), nlv = nrow(HILICPOS),
gs = TRUE,
tol = .Machine$double.eps^0.5, maxit = 200)
## diagram of explained variance
barplot(summary(pcaHILICPOS,X = scale(HILICPOS[,1:dim(HILICPOS)[2]]))$explvar$pvar * 100, names.arg = 1:nrow(HILICPOS), main = "diagram of explained variance - PCA HILIC POS")
## score plot
plotxy(X= pcaHILICPOS$T, group = sample_metadata$Gender,
asp = 0, col = 3:4, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = FALSE,
legend = TRUE, main = "components - PCA HILIC POS", ncol = 1,
pch=16)
## loading plot
plotxy(X= pcaHILICPOS$P, group = NULL,
asp = 0, col = NULL, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = TRUE,
legend = FALSE, main = "loadings - PCA HILIC POS", ncol = 1,
cex=0.8)
MB-PLS-DA model
In MB-PLS-DA, datablocks are separatly scaled, and weigthed by their Frobenius norm. Then, they are concatenated before a PLS-DA to predict or explain a categorical variable. The main steps to apply this method are:
the determination of the optimal number of latent variables of the model, proposed in the package by cross-validation
the model validation, proposed by permutation test
the model analysis, based on the scatter plot, the loading plot, the Variable Importance in Projection
the calculation of the predicted categories for each observation.
In rchemo, all these steps can be performed with a single function. The arguments are:
Xlist: list of training X-data (n, p).
Xnames: names of the X-matrices
Xscaling: vector of Xlist length. X variable scaling among “none” (mean-centering only), “pareto” (mean-centering and pareto scaling), “sd” (mean-centering and unit variance scaling). If “pareto” or “sd”, uncorrected standard deviation is used.
Y: Training Y-data (n, 1)
Yscaling: Y variable scaling among “none” (mean-centering only), “pareto” (mean-centering and pareto scaling), “sd” (mean-centering and unit variance scaling). If “pareto” or “sd”, uncorrected standard deviation is used.
weights Weights (n, 1) to apply to the training observations. Internally, weights are “normalized” to sum to 1. Default to NULL (weights are set to 1/n).
newXlist: list of new X-data (m, p) to consider.
newXnames: names of the newX-matrices
method: method to apply among “mbplsrda”,“mbplslda”,“mbplsqda”
prior: for mbplslda or mbplsqda models : The prior probabilities of the classes. Possible values are “unif” (default; probabilities are set equal for all the classes) or “prop” (probabilities are set equal to the observed proportions of the classes in y).
step: step of the analysis among “nlvtest” (cross-validation to help determine the optimal number of latent variables), “permutation” (permutation test), “model” (model calculation),“prediction” (prediction of newX-data or X-data if any))
nlv: number of latent variables to test if step is “nlvtest”; number of latent variables of the model if step is not “nlvtest”.
modeloutput: if step is “model”: outputs among “scores”, “loadings”, “coef” (regression coefficients), “vip” (Variable Importance in Projection; the VIP calculation being based on the proportion of Y-variance explained by the components, as proposed by Mehmood et al (2012, 2020).)
cvmethod: if step is “nlvtest” or “permutation”: “kfolds” for k-folds cross-validation, or “loo” for leave-one-out.
nbrep: if step is “nlvtest” and cvmethod is “kfolds”: An integer, setting the number of CV repetitions. Default value is 30. Must me set to 1 if cvmethod is “loo”
seed: if step is “nlvtest” and cvmethod is “kfolds”, or if step is “permutation: a numeric. Seed used for the repeated resampling
samplingk: A vector of length n. The elements are the values of a qualitative variable used for stratified partition creation. If NULL, the first observation is set in the first fold, the second observation in the second fold, etc…
nfolds: if cvmethod is “kfolds”. An integer, setting the number of partitions to create.Default value is 10.
npermut: if step is “permutation”: An integer, setting the number of Y-Block with permutated responses to create. Default value is 30.
criterion: if step is “nlvtest” or “permutation” and method is “mbplsrda”, “mbplslda” or “mbplsqda”: optimisation criterion among “rmse” and “err” (for classification error rate)))
selection: if step is “nlvtest”: a character indicating the selection method to use to choose the optimal combination of components, among “localmin”, “globalmin”,“1std”. If “localmin”: the optimal combination corresponds to the first local minimum of the mean CV rmse or error rate. If “globalmin” : the optimal combination corresponds to the minimum mean CV rmse or error rate. If “1std” (one standard error rule) : it corresponds to the first combination after which the mean cross-validated rmse or error rate does not decrease significantly.
determination by cross-validation of the optimal number of latent variables of the model
In this example,the mbplslda method with an uniform prior is performed: a linear discriminant analysis is applied on the PLS scores to obtain the classifications.
In the mbplsrda method, the classification step is performed according to the predicted value, and consequently, it doesn’t take into account the variance of the scatter plot. And the mbplsqda method is mode suited when the scatter plot has an atypical shape.
The cvmethod is to choose according to the number of observations. If this number is small, a leave-one-out cross-validation is more suited, but can lead to optimistic results. In the other cases, it could be better to apply a k-fold cross-validation, usually with 3, 5 or 10 folds. In order to reduce the computational time, in this example, the number of cross- validation repetition is set to 10. But it must be higher (at least 30).
Concerning the criterion, in a discriminant context, it is more logical to choose the classification error rate. However, this can result in an error plot depending on the number of latent variables that is not smooth, so some prefer to use rmsecv instead.
In the example, the selection parameter is set to “localmin”. Normally, the cross-validated error decreases until it reaches the optimal number of latent variables, before rising again. Sometimes it fluctuates before this rise, so choosing “localmin” allows for a more parsimonious model. The “1std” option is also very parsimonious because it only considers a larger number of latent variables if doing so significantly improves the cross-validated error.
nlvtestmbplsda <- mbplsr_mbplsda_allsteps(Xlist = list(GCTOF = GCTOF[,1:dim(GCTOF)[2]],
HILICPOS = HILICPOS[,1:dim(HILICPOS)[2]]),
Xnames = c("GCTOF", "HILICPOS"),
Xscaling = c("none","pareto","sd")[3],
Y = sample_metadata[,"Gender", drop=FALSE],
Yscaling = c("none","pareto","sd")[1],
weights = NULL,
newXlist = NULL, newXnames = NULL,
method = c("mbplsrda","mbplslda","mbplsqda")[2],
prior = c("unif", "prop")[1],
step = c("nlvtest","permutation","model","prediction")[1],
nlv = 4,
#modeloutput = c("scores","loadings","coef","vip"),
cvmethod = c("kfolds","loo")[1],
nbrep = 10,
seed = 123,
samplingk = NULL,
nfolds = 3,
#npermut = 30,
criterion = c("err","rmse")[1],
selection = c("localmin","globalmin","1std")[1],
outputfilename = NULL)
nlvtestmbplsda## nblv err_mean err_sd optimum
## 1 0 0.560294118 0.05162209 0
## 2 1 0.039705882 0.02689386 0
## 3 2 0.008823529 0.01028244 1
## 4 3 0.008823529 0.01028244 0
## 5 4 0.008823529 0.01028244 0nlvoptmbplsda <- nlvtestmbplsda[nlvtestmbplsda$optimum==1,"nblv"] # to obtain the optimal number of LV.
# to plot the results of the cross-validation
plot(nlvtestmbplsda$nblv, nlvtestmbplsda$err_mean, xlab = "number of LV", ylab = "CV classification error rate", pch = 16, ylim = c(0,0.6))
segments(nlvtestmbplsda$nblv,nlvtestmbplsda$err_mean-nlvtestmbplsda$err_sd,nlvtestmbplsda$nblv,nlvtestmbplsda$err_mean+nlvtestmbplsda$err_sd)
segments(nlvtestmbplsda$nblv-0.1,nlvtestmbplsda$err_mean-nlvtestmbplsda$err_sd,nlvtestmbplsda$nblv+0.1,nlvtestmbplsda$err_mean-nlvtestmbplsda$err_sd)
segments(nlvtestmbplsda$nblv-0.1,nlvtestmbplsda$err_mean+nlvtestmbplsda$err_sd,nlvtestmbplsda$nblv+0.1,nlvtestmbplsda$err_mean+nlvtestmbplsda$err_sd)
model validation by permutation test
Usually, the cross-validation parameters are the same than for the determination of the optimal number of latent variables. In this example, as for the determination of the optimal number of latent variables, in order to reduce the computational time, the number of cross- validation repetition and the number of permuted responses are set to 10. But they must be higher (at least 30). To be valid, all the cross-validated errors obtained on permuted data must be lower than the cross-validated error obtained on the original data.
permutmbplsda <- mbplsr_mbplsda_allsteps(Xlist = list(GCTOF = GCTOF[,1:dim(GCTOF)[2]],
HILICPOS = HILICPOS[,1:dim(HILICPOS)[2]]),
Xnames = c("GCTOF", "HILICPOS"),
Xscaling = c("none","pareto","sd")[3],
Y = sample_metadata[,"Gender",drop=FALSE],
Yscaling = c("none","pareto","sd")[1], weights = NULL,
newXlist = NULL, newXnames = NULL,
method = c("mbplsrda","mbplslda","mbplsqda")[2],
prior = c("unif", "prop")[1],
step = c("nlvtest","permutation","model","prediction")[2],
nlv = nlvoptmbplsda,
modeloutput = c("scores","loadings","coef","vip"),
cvmethod = c("kfolds","loo")[1],
nbrep = 10,
seed = 123,
samplingk = NULL,
nfolds = 3,
npermut = 10,
criterion = c("err","rmse")[1],
# selection = c("localmin","globalmin","1std")[1],
import = c("R","ChemFlow","W4M")[1],
outputfilename = NULL)
#plot of the results
plot(permutmbplsda, pch = 16, ylab = "CV classification error rate", xlab = "dyssimilarity Y-Ypermuted")
model analysis, based on the scatter plot, the loading plot, the Variable Importance in Projection
The score plot allows to show the group discrimination. Based on the VIP curve, the threshold to consider that a variable is important can be set.
modelmbplsda <- mbplsr_mbplsda_allsteps(Xlist = list(GCTOF = GCTOF[,1:dim(GCTOF)[2]],
HILICPOS = HILICPOS[,1:dim(HILICPOS)[2]]),
Xnames = c("GCTOF", "HILICPOS"),
Xscaling = c("none","pareto","sd")[3],
Y = sample_metadata[,"Gender",drop=FALSE],
Yscaling = c("none","pareto","sd")[1],
weights = NULL,
newXlist = NULL, newXnames = NULL,
method = c("mbplsrda","mbplslda","mbplsqda")[2],
prior = c("unif", "prop")[1],
step = c("nlvtest","permutation","model","prediction")[3],
nlv = nlvoptmbplsda,
modeloutput = c("scores","loadings","coef","vip"),
cvmethod = c("kfolds","loo")[1],
# nbrep = 30,
# seed = 123,
# samplingk = NULL,
# nfolds = 5,
# npermut = 30,
# criterion = c("err","rmse")[1],
# selection = c("localmin","globalmin","1std")[1],
import = c("R","ChemFlow","W4M")[1],
outputfilename = NULL)
# score plot
plotxy(X= modelmbplsda$scores, group = sample_metadata$Gender,
asp = 0, col = 3:4, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = FALSE,
legend = TRUE, main = "scores - MB PLS DA", ncol = 1,
pch=16)
# loading plot
plotxy(X= modelmbplsda$loadings, group = substr(rownames(modelmbplsda$loadings),1,6),
asp = 0, col = NULL, alpha.f = .8,
zeroes = TRUE, circle = FALSE, ellipse = FALSE,
labels = FALSE,
legend = TRUE, main = "loadings - MB PLS DA", ncol = 1,
cex=0.8, pch = 16)
# VIP curve
plot(modelmbplsda$vip[order(modelmbplsda$vip[,nlvoptmbplsda], decreasing = TRUE),nlvoptmbplsda], pch = 16,cex = 0.8,
col = as.numeric(as.factor(substr(rownames(modelmbplsda$vip[order(modelmbplsda$vip[,nlvoptmbplsda], decreasing = TRUE),nlvoptmbplsda, drop=FALSE]),1,6))), ylab = "VIP value",
main = "VIP curve MB PLS DA")
legend("topright", legend = c("GCTOF", "HILICPOS"), pch = 16, col = 1:2)
predicted values
The prediction step provides a table with:
subjects scores
predicted categories
probabilities to be predicted for each category.
predmbplsda <- mbplsr_mbplsda_allsteps(Xlist = list(GCTOF = GCTOF[,1:dim(GCTOF)[2]],
HILICPOS = HILICPOS[,1:dim(HILICPOS)[2]]),
Xnames = c("GCTOF", "HILICPOS"),
Xscaling = c("none","pareto","sd")[3],
Y = sample_metadata[,"Gender",drop=FALSE],
Yscaling = c("none","pareto","sd")[1],
weights = NULL,
newXlist = NULL, newXnames = NULL,
method = c("mbplsrda","mbplslda","mbplsqda")[2],
prior = c("unif", "prop")[1],
step = c("nlvtest","permutation","model","prediction")[4],
nlv = nlvoptmbplsda,
# modeloutput = c("scores","loadings","coef","vip"),
#
# cvmethod = c("kfolds","loo")[1],
# nbrep = 30,
# seed = 123,
# samplingk = NULL,
# nfolds = 5,
# npermut = 30,
#
# criterion = c("err","rmse")[1],
# selection = c("localmin","globalmin","1std")[1],
import = c("R","ChemFlow","W4M")[1],
outputfilename = NULL)
predmbplsda## lv1 lv2 pred.y1 pred.posterior.Female
## wM_001 0.54558754 -0.3480701786 Male 3.021370e-22
## wM_002 0.27672623 0.5525506059 Male 6.644988e-23
## wF_003 -0.18953500 -0.6066209461 Female 1.000000e+00
## wF_004 -0.25792171 -0.1626404652 Female 1.000000e+00
## wM_005 0.56744443 0.1747950458 Male 1.129001e-31
## wM_006 0.41047657 0.3127838504 Male 6.872642e-26
## wM_007 0.62432444 0.0665651227 Male 7.633840e-33
## wF_008 -0.26793088 -0.5210826748 Female 1.000000e+00
## wF_009 -0.43812743 0.7033443778 Female 1.000000e+00
## wF_010 -0.36240950 -0.1472302702 Female 1.000000e+00
## wM_011 0.68346912 -0.3273525088 Male 1.385751e-29
## wM_012 0.45290904 -0.0350832487 Male 1.633604e-22
## wM_013 0.24736228 -0.1652307834 Male 5.393351e-10
## wF_014 -0.20535172 -0.7695462248 Female 1.000000e+00
## wF_015 -0.25984530 -0.4444141502 Female 1.000000e+00
## wF_016 -0.78621166 1.1800474687 Female 1.000000e+00
## wM_017 0.37249331 0.0913761085 Male 1.947827e-20
## wM_018 0.36660722 0.2772086830 Male 4.295314e-23
## wM_019 0.33774376 0.1574541099 Male 1.011542e-19
## wM_020 0.34257086 -0.0126229122 Male 2.915889e-17
## wM_021 0.42810439 0.1353859046 Male 5.789615e-24
## wF_022 -0.42117471 -0.1965165871 Female 1.000000e+00
## wF_023 -0.43007949 -0.0829182271 Female 1.000000e+00
## wF_024 -0.30443954 -0.3161993062 Female 1.000000e+00
## wF_025 -0.27525802 -0.4767367782 Female 1.000000e+00
## wF_026 -0.42887830 -0.3696893442 Female 1.000000e+00
## wM_027 0.23855883 0.7513316279 Male 3.989847e-24
## wM_028 0.54189604 -0.1226002419 Male 1.206804e-25
## wM_029 0.47860932 0.1794120552 Male 3.126452e-27
## wF_030 -0.30062152 -0.3746063899 Female 1.000000e+00
## wF_031 -0.63819763 0.1374083309 Female 1.000000e+00
## wF_032 -0.51121074 0.2163930345 Female 1.000000e+00
## wM_033 0.43275430 -0.1176136958 Male 3.551174e-20
## wM_034 0.56214830 -0.1994148151 Male 1.878976e-25
## wF_036 -0.34102658 -0.5445495665 Female 1.000000e+00
## wF_037 -0.24651172 -0.7841320956 Female 1.000000e+00
## wF_038 -0.15350386 -0.3413986114 Female 1.000000e+00
## wM_039 0.24214357 0.2142606496 Male 9.143881e-16
## wF_040 -0.15144467 -1.0875471713 Female 1.000000e+00
## mM_077 0.45765804 0.2197480622 Male 8.289178e-27
## mM_078 0.51978319 0.0272823009 Male 6.633571e-27
## mM_079 0.40675803 0.3043368636 Male 1.447116e-25
## mF_080 -0.46775285 -0.0005502785 Female 1.000000e+00
## mF_081 -0.77371976 0.7389887822 Female 1.000000e+00
## mF_082 -0.73247181 0.7521846206 Female 1.000000e+00
## mM_101 0.59862750 -0.2587550942 Male 2.308859e-26
## mM_103 -0.01715897 1.5414920887 Male 1.076581e-23
## mF_104 -0.38675396 -0.1153383479 Female 1.000000e+00
## mF_105 -0.53988268 0.1643913533 Female 1.000000e+00
## mF_106 -0.43159893 -0.0493457028 Female 1.000000e+00
## mM_173 0.28114216 0.5823233714 Male 1.331882e-23
## mM_174 0.56080465 -0.3801265587 Male 1.646418e-22
## mM_175 0.38261063 -0.0586969348 Male 1.452927e-18
## mF_176 -0.48741429 0.0046199111 Female 1.000000e+00
## mF_177 -0.58208729 0.1995090610 Female 1.000000e+00
## mF_178 -0.49321891 0.2434577064 Female 1.000000e+00
## mM_203 0.56597280 -0.0499160055 Male 5.030964e-28
## mM_204 0.47625034 -0.1217012783 Male 2.537079e-22
## mM_205 0.50231341 0.1538464184 Male 4.974237e-28
## mF_206 -0.11621764 -0.3973940955 Female 1.000000e+00
## mF_207 -0.51776158 -0.0145000918 Female 1.000000e+00
## mF_208 -0.47720999 -0.0883721908 Female 1.000000e+00
## mM_209 0.41289099 0.2703443875 Male 2.451390e-25
## mM_210 0.33125672 0.3419254886 Male 2.515514e-22
## mM_211 0.33599218 0.4426191774 Male 3.616769e-24
## mF_212 -0.34935922 0.1392809556 Female 1.000000e+00
## mF_213 -0.41441692 -0.1738904810 Female 1.000000e+00
## mF_214 -0.22728541 -1.0142632710 Female 1.000000e+00
## pred.posterior.Male
## wM_001 1.000000e+00
## wM_002 1.000000e+00
## wF_003 1.092976e-20
## wF_004 4.207508e-17
## wM_005 1.000000e+00
## wM_006 1.000000e+00
## wM_007 1.000000e+00
## wF_008 2.594243e-23
## wF_009 1.727822e-12
## wF_010 3.611270e-22
## wM_011 1.000000e+00
## wM_012 1.000000e+00
## wM_013 1.000000e+00
## wF_014 4.397232e-24
## wF_015 1.107853e-21
## wF_016 1.334751e-22
## wM_017 1.000000e+00
## wM_018 1.000000e+00
## wM_019 1.000000e+00
## wM_020 1.000000e+00
## wM_021 1.000000e+00
## wF_022 6.116427e-26
## wF_023 1.382545e-24
## wF_024 6.560388e-22
## wF_025 5.583315e-23
## wF_026 4.370119e-29
## wM_027 1.000000e+00
## wM_028 1.000000e+00
## wM_029 1.000000e+00
## wF_030 1.207860e-22
## wF_031 1.163407e-31
## wF_032 5.986934e-24
## wM_033 1.000000e+00
## wM_034 1.000000e+00
## wF_036 2.113745e-27
## wF_037 2.083913e-26
## wF_038 1.226588e-14
## wM_039 1.000000e+00
## wF_040 2.115853e-26
## mM_077 1.000000e+00
## mM_078 1.000000e+00
## mM_079 1.000000e+00
## mF_080 3.433359e-25
## mF_081 5.560755e-29
## mF_082 1.126667e-26
## mM_101 1.000000e+00
## mM_103 1.000000e+00
## mF_104 6.720559e-23
## mF_105 3.108831e-26
## mF_106 3.957580e-24
## mM_173 1.000000e+00
## mM_174 1.000000e+00
## mM_175 1.000000e+00
## mF_176 4.154279e-26
## mF_177 8.049299e-28
## mF_178 1.325162e-22
## mM_203 1.000000e+00
## mM_204 1.000000e+00
## mM_205 1.000000e+00
## mF_206 1.240074e-13
## mF_207 5.911871e-28
## mF_208 4.551203e-27
## mM_209 1.000000e+00
## mM_210 1.000000e+00
## mM_211 1.000000e+00
## mF_212 6.000164e-17
## mF_213 3.089580e-25
## mF_214 4.323746e-29Reproducibility
This vignette was produced with the following R session configuration.
## R version 4.6.0 (2026-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] rchemo_0.1-4 knitr_1.51
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.6 rlang_1.2.0 xfun_0.58 jsonlite_2.0.0
## [5] data.table_1.18.4 buildtools_1.0.0 htmltools_0.5.9 maketools_1.3.2
## [9] e1071_1.7-17 sys_3.4.3 sass_0.4.10 rmarkdown_2.31
## [13] evaluate_1.0.5 jquerylib_0.1.4 MASS_7.3-65 fastmap_1.2.0
## [17] yaml_2.3.12 lifecycle_1.0.5 FNN_1.1.4.1 compiler_4.6.0
## [21] digest_0.6.39 signal_1.8-1 R6_2.6.1 class_7.3-23
## [25] bslib_0.11.0 tools_4.6.0 proxy_0.4-29 cachem_1.1.0