Hello TeamMixOmics,
first of all thank you very much for your work, this package is really awesome.
I have been using it for quite a while with almost zero issues but lately I am experiencing this bug: the perf function applied to a block.splsda object seems to no fill up the slot AveragedPredict.class, like in the attached example.
Am I missing some update? am I using a wrong version of the package? I doublechecked the sessionInfo and I have the impression I am up-to-date but maybe you can help me seeing a mistake I missed!
## loading library mixOmics
library(mixOmics)
#> Loading required package: MASS
#> Loading required package: lattice
#> Loading required package: ggplot2
#>
#> Loaded mixOmics 6.15.26
#> Thank you for using mixOmics!
#> Tutorials: http://mixomics.org
#> Bookdown vignette: https://mixomicsteam.github.io/Bookdown
#> Questions, issues: Follow the prompts at http://mixomics.org/contact-us
#> Cite us: citation('mixOmics')
data("breast.TCGA")
## this is the X data as a list of mRNA, miRNA and proteins
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna,
protein = breast.TCGA$data.train$protein)
## set up a full design where every block is connected
design = matrix(1, ncol = length(data), nrow = length(data),
dimnames = list(names(data), names(data)))
diag(design) = 0
design
#> mrna mirna protein
#> mrna 0 1 1
#> mirna 1 0 1
#> protein 1 1 0
## set number of variables to select
list.keepX = list(mrna =20, mirna =2, protein = 10)
TCGA.block.splsda = block.splsda(X = data, Y = breast.TCGA$data.train$subtype,
ncomp = 1, keepX = list.keepX, design = design)
#> Design matrix has changed to include Y; each block will be
#> linked to Y.
perf(TCGA.block.splsda) -> l
## this function perf does not fill up the slot AveragedPredict.class
l$AveragedPredict.class
#> list()
Created on 2020-12-11 by the reprex package (v0.3.0.9001)
Session info
sessioninfo::session_info()
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#> setting value
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#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
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#> tz Europe/Paris
#> date 2020-12-11
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#> BiocParallel 1.22.0 2020-04-27 [1]
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#> stringr 1.4.0 2019-02-10 [1]
#> styler 1.3.2 2020-02-23 [1]
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