o2plsda provides functions to do O2PLS-DA analysis for multiple omics integration.The algorithm came from “O2-PLS, a two-block (X±Y) latent variable regression (LVR) method with an integral OSC filter” which published by Johan Trygg and Svante Wold at 2003. O2PLS is a bidirectional multivariate regression method that aims to separate the covariance between two data sets (it was recently extended to multiple data sets) (Löfstedt and Trygg, 2011; Löfstedt et al., 2012) from the systematic sources of variance being specific for each data set separately.
In order to avoid overfitting of the model, the optimal number of latent variables for each model structure was estimated using group-balanced MCCV. The package could use the group information when we select the best paramaters with cross-validation. In cross-validation (CV) one minimizes a certain measure of error over some parameters that should be determined a priori. Here, we have three parameters: (nc, nx, ny). A popular measure is the prediction error ||Y - ||, where is a prediction of Y. In our case the O2PLS method is symmetric in X and Y, so we minimize the sum of the prediction errors: ||X - ||+||Y - ||.
And we also calculate the the average Q^2 values:
Q^2 = 1 - err / Var_{total};
err = Var_{expected} - Var_{estimated};
Here nc should be a positive integer, and nx and ny should be non-negative. The best integers are then the minimizers of the prediction error.
The O2PLS-DA analysis was performed as described by Bylesjö et al. (2007); briefly, the O2PLS predictive variation [\(TW^\top\), \(UC^\top\)] was used for a subsequent O2PLS-DA analysis. The Variable Importance in the Projection (VIP) value was calculated as a weighted sum of the squared correlations between the OPLS-DA components and the original variable.
library(devtools)
install_github("guokai8/o2plsda")library(o2plsda)
set.seed(123)
# sample * values
X = matrix(rnorm(5000),50,100)
# sample * values
Y = matrix(rnorm(5000),50,100)
rownames(X) <- paste("S",1:50,sep="")
rownames(Y) <- paste("S",1:50,sep="")
colnames(X) <- paste("Gene",1:100,sep="")
colnames(Y) <- paste("Lipid",1:100,sep="")
X = scale(X, scale=T)
Y = scale(Y, scale=T)
## group factor could be omitted if you don't have any group
group <- rep(c("Ctrl","Treat"),each = 25)Do cross validation with group information
set.seed(123)
## nr_folds : cross validation k-fold (suggest 10)
## ncores : parallel paramaters for large datasets
cv <- o2cv(X,Y,1:5,1:3,1:3,group=group,nr_folds = 10)
#####################################
The best parameters are nc = 5, nx = 3, ny = 3
#####################################
The Qxy is 0.073901318688517 and the RMSE is: 2.02464376258545
#####################################Then we can do the O2PLS analysis with nc = 5, nx = 3, ny =3. You can also select the best paramaters by looking at the cross validation results.
fit <- o2pls(X,Y,5,2,3)
summary(fit)
######### Summary of the O2PLS results #########
### Call o2pls(X, Y, nc= 5 , nx= 2 , ny= 3 ) ###
### Total variation
### X: 4900 ; Y: 4900 ###
### Total modeled variation ### X: 0.261 ; Y: 0.314 ###
### Joint, Orthogonal, Noise (proportions) ###
X Y
Joint 0.186 0.199
Orthogonal 0.075 0.115
Noise 0.739 0.686
### Variation in X joint part predicted by Y Joint part: 0.901
### Variation in Y joint part predicted by X Joint part: 0.902
### Variation in each Latent Variable (LV) in Joint part:
LV1 LV2 LV3 LV4 LV5
X 0.039 0.040 0.040 0.034 0.033
Y 0.049 0.043 0.036 0.037 0.033
### Variation in each Latent Variable (LV) in X Orthogonal part:
LV1 LV2
X 0.04 0.036
### Variation in each Latent Variable (LV) in Y Orthogonal part:
LV1 LV2 LV3
Y 0.045 0.037 0.034
############################################
Extract the loadings and scores from the fit results
Xl <- loadings(fit,loading="Xjoint")
Xs <- scores(fit,score="Xjoint")
plot(fit,type="score",var="Xjoint", group=group)
plot(fit,type="loading",var="Xjoint", group=group,repel=F,rotation=TRUE)Do the OPLSDA based on the O2PLS results
res <- oplsda(fit,group, nc=5)
plot(res,type="score", group=group)
vip <- vip(res)
plot(res,type="vip", group = group, repel = FALSE,order=TRUE)The package is still under development.
If you like this package, please contact me for the citation.
For any questions please contact guokai8@gmail.com or https://github.com/guokai8/o2plsda/issues