Vignette of the a4Classif package

Introduction

This document explains the functionalities available in the a4Classif package.

This package contains for classification of Affymetrix microarray data, stored in an ExpressionSet. This package integrates within the Automated Affymetrix Array Analysis suite of packages.

## Loading required package: a4Core
## Loading required package: a4Preproc
## 
## a4Classif version 1.53.0
## Loading required package: Biobase
## Loading required package: BiocGenerics
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## Welcome to Bioconductor
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##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.

To demonstrate the functionalities of the package, the ALL dataset is used. The genes are annotated thanks to the addGeneInfo utility function of the a4Preproc package.

data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
## Loading required package: hgu95av2.db
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: IRanges
## Loading required package: S4Vectors
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## Attaching package: 'S4Vectors'
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## 
ALL$BTtype <- as.factor(substr(ALL$BT,0,1))

Classify microarray data

Lasso regression

resultLasso <- lassoClass(object = ALL, groups = "BTtype")
plot(resultLasso, 
    label = TRUE, 
    main = "Lasso coefficients in relation to degree of penalization."
)

topTable(resultLasso, n = 15)
## The lasso selected 16 genes. The top 15 genes are:
## 
##             Gene Coefficient
## 38319_at    CD3D  0.95966733
## 35016_at    CD74 -0.60928095
## 38147_at  SH2D1A  0.49240967
## 35792_at    MGLL  0.46856925
## 37563_at  SRGAP3  0.26648240
## 38917_at  YME1L1  0.25100075
## 40278_at    GGA2 -0.25017550
## 41164_at    IGHM -0.12387272
## 41409_at THEMIS2 -0.10581122
## 38242_at    BLNK -0.10309606
## 35523_at   HPGDS  0.10169706
## 38949_at   PRKCQ  0.07832802
## 33316_at     TOX  0.06963509
## 33839_at   ITPR2  0.05801832
## 40570_at   FOXO1 -0.04858863

PAM regression

resultPam <- pamClass(object = ALL, groups = "BTtype")
plot(resultPam, 
    main = "Pam misclassification error versus number of genes."
)

topTable(resultPam, n = 15)
## Pam selected  1  genes. The top  15  genes are:
## 
##          GeneSymbol B.score T.score av.rank.in.CV prop.selected.in.CV
## 38319_at       CD3D -0.1693  0.4875             1                   1
confusionMatrix(resultPam)
##     predicted
## true  B  T
##    B 95  0
##    T  1 32

Random forest

# select only a subset of the data for computation time reason
ALLSubset <- ALL[sample.int(n = nrow(ALL), size = 100, replace = FALSE), ]

resultRf <- rfClass(object = ALLSubset, groups = "BTtype")
plot(resultRf)

topTable(resultRf, n = 15)
## Random forest selected 17 genes. The top 15 genes are:
## 
##            GeneSymbol
## 31682_s_at       VCAN
## 31731_at         CBX4
## 32046_at        PRKCD
## 32332_at         IDH2
## 32833_at         CLK1
## 33770_at         CHUK
## 34671_at       POLR3C
## 34707_at         CHD3
## 35209_at         <NA>
## 36143_at        CASP3
## 36366_at      B4GALT6
## 37988_at        CD79B
## 38650_at       IGFBP5
## 40271_at        NUP93
## 40505_at       UBE2L6

ROC curve

ROCcurve(gene = "ABL1", object = ALL, groups = "BTtype")
## Warning in ROCcurve(gene = "ABL1", object = ALL, groups = "BTtype"): Gene ABL1 corresponds to 6 probesets; only the first probeset ( 1635_at ) has been displayed on the plot.

Appendix

Session information

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
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## 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
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## time zone: Etc/UTC
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
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## other attached packages:
##  [1] hgu95av2.db_3.13.0   org.Hs.eg.db_3.19.1  AnnotationDbi_1.67.0 IRanges_2.39.2       S4Vectors_0.43.2     ALL_1.47.0           Biobase_2.65.1       BiocGenerics_0.51.0  a4Classif_1.53.0     a4Preproc_1.53.0     a4Core_1.53.0        rmarkdown_2.28      
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## [41] R6_2.5.1                lifecycle_1.0.4         zlibbioc_1.51.1         KEGGREST_1.45.1         randomForest_4.7-1.1    bit_4.0.5               cluster_2.1.6           pkgconfig_2.0.3         bslib_0.8.0             Rcpp_1.0.13             highr_0.11              xfun_0.47               sys_3.4.2               knitr_1.48              htmltools_0.5.8.1       maketools_1.3.0         compiler_4.4.1