This code block is not evaluated. Need a breakdown? Look at the following sections.
suppressWarnings(suppressMessages(require(netDx)))
suppressWarnings(suppressMessages(library(curatedTCGAData)))
# fetch RNA, methylation and proteomic data for TCGA BRCA set
brca <- suppressMessages(
curatedTCGAData("BRCA",
c("mRNAArray","RPPA*","Methylation_methyl27*"),
dry.run=FALSE))
# process input variables
# prepare clinical variable - stage
staget <- sub("[abcd]","",sub("t","",colData(brca)$pathology_T_stage))
staget <- suppressWarnings(as.integer(staget))
colData(brca)$STAGE <- staget
# exclude normal, HER2 (small num samples)
pam50 <- colData(brca)$PAM50.mRNA
idx <- union(which(pam50 %in% c("Normal-like","HER2-enriched")),
which(is.na(staget)))
idx <- union(idx, which(is.na(pam50)))
pID <- colData(brca)$patientID
tokeep <- setdiff(pID, pID[idx])
brca <- brca[,tokeep,]
pam50 <- colData(brca)$PAM50.mRNA
colData(brca)$pam_mod <- pam50
# remove duplicate names
smp <- sampleMap(brca)
for (nm in names(brca)) {
samps <- smp[which(smp$assay==nm),]
notdup <- samps[which(!duplicated(samps$primary)),"colname"]
brca[[nm]] <- suppressMessages(brca[[nm]][,notdup])
}
# colData must have ID and STATUS columns
pID <- colData(brca)$patientID
colData(brca)$ID <- pID
colData(brca)$STATUS <- gsub(" ","_",colData(brca)$pam_mod)
# create grouping rules
groupList <- list()
# genes in mRNA data are grouped by pathways
pathList <- readPathways(fetchPathwayDefinitions("January",2018))
groupList[["BRCA_mRNAArray-20160128"]] <- pathList[1:3]
# clinical data is not grouped; each variable is its own feature
groupList[["clinical"]] <- list(
age="patient.age_at_initial_pathologic_diagnosis",
stage="STAGE"
)
# for methylation generate one feature containing all probes
# same for proteomics data
tmp <- list(rownames(experiments(brca)[[2]]));
names(tmp) <- names(brca)[2]
groupList[[names(brca)[2]]] <- tmp
tmp <- list(rownames(experiments(brca)[[3]]));
names(tmp) <- names(brca)[3]
groupList[[names(brca)[3]]] <- tmp
# create function to tell netDx how to build features
# (PSN) from your data
makeNets <- function(dataList, groupList, netDir,...) {
netList <- c() # initialize before is.null() check
# correlation-based similarity for mRNA, RPPA and methylation data
# (Pearson correlation)
for (nm in setdiff(names(groupList),"clinical")) {
# NOTE: the check for is.null() is important!
if (!is.null(groupList[[nm]])) {
netList <- makePSN_NamedMatrix(dataList[[nm]],
rownames(dataList[[nm]]),
groupList[[nm]],netDir,verbose=FALSE,
writeProfiles=TRUE,...)
}
}
# make clinical nets (normalized difference)
netList2 <- c()
if (!is.null(groupList[["clinical"]])) {
netList2 <- makePSN_NamedMatrix(dataList$clinical,
rownames(dataList$clinical),
groupList[["clinical"]],netDir,
simMetric="custom",customFunc=normDiff, # custom function
writeProfiles=FALSE,
sparsify=TRUE,verbose=TRUE,...)
}
netList <- c(unlist(netList),unlist(netList2))
return(netList)
}
# run predictor
set.seed(42) # make results reproducible
outDir <- paste(tempdir(),randAlphanumString(),"pred_output",sep=getFileSep())
# To see all messages, remove suppressMessages()
# and set logging="default".
# To keep all intermediate data, set keepAllData=TRUE
numSplits <- 2L
out <- suppressMessages(
buildPredictor(dataList=brca,groupList=groupList,
makeNetFunc=makeNets,
outDir=outDir, ## netDx requires absolute path
numSplits=numSplits, featScoreMax=2L, featSelCutoff=1L,
numCores=1L)
)
# collect results for accuracy
st <- unique(colData(brca)$STATUS)
acc <- matrix(NA,ncol=length(st),nrow=numSplits) # accuracy by class
colnames(acc) <- st
for (k in 1:numSplits) {
pred <- out[[sprintf("Split%i",k)]][["predictions"]];
tmp <- pred[,c("ID","STATUS","TT_STATUS","PRED_CLASS",
sprintf("%s_SCORE",st))]
for (m in 1:length(st)) {
tmp2 <- subset(tmp, STATUS==st[m])
acc[k,m] <- sum(tmp2$PRED==tmp2$STATUS)/nrow(tmp2)
}
}
# accuracy by class
print(round(acc*100,2))
# confusion matrix
res <- out$Split1$predictions
print(table(res[,c("STATUS","PRED_CLASS")]))
sessionInfo()
In this example, we will use clinical data and three types of 'omic data - gene expression, DNA methylation and proteomic data - to classify breast tumours as being one of three types: Luminal A, Luminal B, or Basal. This example is nearly identical to the one used to build a binary classifier.
We also use several strategies and definitions of similarity to create features:
Load the netDx package.
suppressWarnings(suppressMessages(require(netDx)))
For this example we pull data from the The Cancer Genome Atlas through the BioConductor curatedTCGAData package. The fetch command automatically brings in a MultiAssayExperiment object.
suppressMessages(library(curatedTCGAData))
We use the curatedTCGAData() command to look at available assays in the breast cancer dataset.
curatedTCGAData(diseaseCode="BRCA", assays="*",dry.run=TRUE)
## snapshotDate(): 2020-10-02
## See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
## ah_id title file_size
## 1 EH584 BRCA_CNASeq-20160128 0 Mb
## 2 EH585 BRCA_CNASNP-20160128 9.8 Mb
## 3 EH586 BRCA_CNVSNP-20160128 2.8 Mb
## 4 EH588 BRCA_GISTIC_AllByGene-20160128 1.3 Mb
## 5 EH2121 BRCA_GISTIC_Peaks-20160128 0 Mb
## 6 EH589 BRCA_GISTIC_ThresholdedByGene-20160128 0.4 Mb
## 7 EH2122 BRCA_Methylation_methyl27-20160128_assays 63.2 Mb
## 8 EH2123 BRCA_Methylation_methyl27-20160128_se 0.4 Mb
## 9 EH2124 BRCA_Methylation_methyl450-20160128_assays 2613.2 Mb
## 10 EH2125 BRCA_Methylation_methyl450-20160128_se 6.1 Mb
## 11 EH593 BRCA_miRNASeqGene-20160128 0.6 Mb
## 12 EH594 BRCA_mRNAArray-20160128 27.3 Mb
## 13 EH595 BRCA_Mutation-20160128 4.5 Mb
## 14 EH596 BRCA_RNASeq2GeneNorm-20160128 64.5 Mb
## 15 EH597 BRCA_RNASeqGene-20160128 30 Mb
## 16 EH598 BRCA_RPPAArray-20160128 1.6 Mb
## rdataclass rdatadateadded rdatadateremoved
## 1 RaggedExperiment 2017-10-10 <NA>
## 2 RaggedExperiment 2017-10-10 <NA>
## 3 RaggedExperiment 2017-10-10 <NA>
## 4 SummarizedExperiment 2017-10-10 <NA>
## 5 RangedSummarizedExperiment 2019-01-09 <NA>
## 6 SummarizedExperiment 2017-10-10 <NA>
## 7 SummarizedExperiment 2019-01-09 <NA>
## 8 SummarizedExperiment 2019-01-09 <NA>
## 9 RaggedExperiment 2019-01-09 <NA>
## 10 SummarizedExperiment 2019-01-09 <NA>
## 11 SummarizedExperiment 2017-10-10 <NA>
## 12 SummarizedExperiment 2017-10-10 <NA>
## 13 RaggedExperiment 2017-10-10 <NA>
## 14 SummarizedExperiment 2017-10-10 <NA>
## 15 SummarizedExperiment 2017-10-10 <NA>
## 16 SummarizedExperiment 2017-10-10 <NA>
In this call we fetch only the gene expression, proteomic and methylation data; setting dry.run=FALSE initiates the fetching of the data.
brca <- suppressMessages(
curatedTCGAData("BRCA",
c("mRNAArray","RPPA*","Methylation_methyl27*"),
dry.run=FALSE))
This next code block prepares the TCGA data. In practice you would do this once, and save the data before running netDx, but we run it here to see an end-to-end example.
# prepare clinical variable - stage
staget <- sub("[abcd]","",sub("t","",colData(brca)$pathology_T_stage))
staget <- suppressWarnings(as.integer(staget))
colData(brca)$STAGE <- staget
# exclude normal, HER2 (small num samples)
pam50 <- colData(brca)$PAM50.mRNA
idx <- union(which(pam50 %in% c("Normal-like","HER2-enriched")),
which(is.na(staget)))
idx <- union(idx, which(is.na(pam50)))
pID <- colData(brca)$patientID
tokeep <- setdiff(pID, pID[idx])
brca <- brca[,tokeep,]
pam50 <- colData(brca)$PAM50.mRNA
colData(brca)$pam_mod <- pam50
# remove duplicate names
smp <- sampleMap(brca)
for (nm in names(brca)) {
samps <- smp[which(smp$assay==nm),]
notdup <- samps[which(!duplicated(samps$primary)),"colname"]
brca[[nm]] <- suppressMessages(brca[[nm]][,notdup])
}
## harmonizing input:
## removing 59 sampleMap rows with 'colname' not in colnames of experiments
## harmonizing input:
## removing 19 sampleMap rows with 'colname' not in colnames of experiments
## harmonizing input:
## removing 26 sampleMap rows with 'colname' not in colnames of experiments
The important thing is to create ID and STATUS columns in the sample metadata slot. netDx uses these to get the patient identifiers and labels, respectively.
pID <- colData(brca)$patientID
colData(brca)$ID <- pID
colData(brca)$STATUS <- gsub(" ","_",colData(brca)$pam_mod)
Our plan is to group gene expression data by pathways and clinical data by single variables. We will treat methylation and proteomic data each as a single feature, so each of those groups will contain the entire input table for those corresponding data types.
In the code below, we fetch pathway definitions for January 2018 from (http://download.baderlab.org/EM_Genesets) and group gene expression data by pathways. To keep the example short, we limit to only three pathways, but in practice you would use all pathways meeting a size criterion; e.g. those containing between 10 and 500 genes.
Grouping rules are accordingly created for the clinical, methylation and proteomic data.
groupList <- list()
# genes in mRNA data are grouped by pathways
pathList <- readPathways(fetchPathwayDefinitions("January",2018))
## ---------------------------------------
## Fetching http://download.baderlab.org/EM_Genesets/January_01_2018/Human/symbol/Human_AllPathways_January_01_2018_symbol.gmt
## File: 12bc4b4f1937_Human_AllPathways_January_01_2018_symbol.gmt
## Read 3028 pathways in total, internal list has 3009 entries
## FILTER: sets with num genes in [10, 200]
## => 971 pathways excluded
## => 2038 left
groupList[["BRCA_mRNAArray-20160128"]] <- pathList[1:3]
# clinical data is not grouped; each variable is its own feature
groupList[["clinical"]] <- list(
age="patient.age_at_initial_pathologic_diagnosis",
stage="STAGE"
)
# for methylation generate one feature containing all probes
# same for proteomics data
tmp <- list(rownames(experiments(brca)[[2]]));
names(tmp) <- names(brca)[2]
groupList[[names(brca)[2]]] <- tmp
tmp <- list(rownames(experiments(brca)[[3]]));
names(tmp) <- names(brca)[3]
groupList[[names(brca)[3]]] <- tmp
We provide netDx with a custom function to generate similarity networks (i.e. features). The first block tells netDx to generate correlation-based networks using everything but the clinical data. This is achieved by the call:
makePSN_NamedMatrix(..., writeProfiles=TRUE,...)`
The second block makes a different call to makePSN_NamedMatrix() but this time, requesting the use of the normalized difference similarity metric. This is achieved by calling:
makePSN_NamedMatrix(,...,
simMetric="custom", customFunc=normDiff,
writeProfiles=FALSE)
normDiff is a function provided in the netDx package, but the user may define custom similarity functions in this block of code and pass those to makePSN_NamedMatrix(), using the customFunc parameter.
makeNets <- function(dataList, groupList, netDir,...) {
netList <- c() # initialize before is.null() check
# correlation-based similarity for mRNA, RPPA and methylation data
# (Pearson correlation)
for (nm in setdiff(names(groupList),"clinical")) {
# NOTE: the check for is.null() is important!
if (!is.null(groupList[[nm]])) {
netList <- makePSN_NamedMatrix(dataList[[nm]],
rownames(dataList[[nm]]),
groupList[[nm]],netDir,verbose=FALSE,
writeProfiles=TRUE,...)
}
}
# make clinical nets (normalized difference)
netList2 <- c()
if (!is.null(groupList[["clinical"]])) {
netList2 <- makePSN_NamedMatrix(dataList$clinical,
rownames(dataList$clinical),
groupList[["clinical"]],netDir,
simMetric="custom",customFunc=normDiff, # custom function
writeProfiles=FALSE,
sparsify=TRUE,verbose=TRUE,...)
}
netList <- c(unlist(netList),unlist(netList2))
return(netList)
}
Finally we make the call to build the predictor.
set.seed(42) # make results reproducible
# location for intermediate work
# set keepAllData to TRUE to not delete at the end of the
# predictor run.
# This can be useful for debugging.
outDir <- paste(tempdir(),"pred_output",sep=getFileSep()) # use absolute path
numSplits <- 2L
out <- suppressMessages(
buildPredictor(dataList=brca,groupList=groupList,
makeNetFunc=makeNets,
outDir=outDir, ## netDx requires absolute path
numSplits=numSplits, featScoreMax=2L, featSelCutoff=1L,
numCores=1L)
)
## function(dataList, groupList, netDir,...) {
## netList <- c() # initialize before is.null() check
## # correlation-based similarity for mRNA, RPPA and methylation data
## # (Pearson correlation)
## for (nm in setdiff(names(groupList),"clinical")) {
## # NOTE: the check for is.null() is important!
## if (!is.null(groupList[[nm]])) {
## netList <- makePSN_NamedMatrix(dataList[[nm]],
## rownames(dataList[[nm]]),
## groupList[[nm]],netDir,verbose=FALSE,
## writeProfiles=TRUE,...)
## }
## }
##
## # make clinical nets (normalized difference)
## netList2 <- c()
## if (!is.null(groupList[["clinical"]])) {
## netList2 <- makePSN_NamedMatrix(dataList$clinical,
## rownames(dataList$clinical),
## groupList[["clinical"]],netDir,
## simMetric="custom",customFunc=normDiff, # custom function
## writeProfiles=FALSE,
## sparsify=TRUE,verbose=TRUE,...)
## }
## netList <- c(unlist(netList),unlist(netList2))
## return(netList)
## }
## IS_TRAIN
## STATUS TRAIN TEST
## Basal-like 77 20
## Luminal_A 184 46
## Luminal_B 101 26
##
## Luminal_A nonpred <NA>
## 184 178 0
##
## Basal-like nonpred <NA>
## 77 285 0
##
## Luminal_B nonpred <NA>
## 101 261 0
## IS_TRAIN
## STATUS TRAIN TEST
## Basal-like 77 20
## Luminal_A 184 46
## Luminal_B 101 26
##
## Luminal_A nonpred <NA>
## 184 178 0
##
## Basal-like nonpred <NA>
## 77 285 0
##
## Luminal_B nonpred <NA>
## 101 261 0
The results are stored in the list object returned by the buildPredictor() call.
This list contains:
inputNets: all input networks that the model started with. Split<i>: a list with results for each train-test split
featureScores: feature scores for each label (list with g entries, where g is number of patient labels). Each entry contains the feature selection scores for the corresponding label.featureSelected: vector of features that pass feature selection. List of length g, with one entry per label.predictions: real and predicted labels for test patientsaccuracy: percent accuracy of predictionssummary(out)
## Length Class Mode
## inputNets 14 -none- character
## Split1 4 -none- list
## Split2 4 -none- list
summary(out$Split1)
## Length Class Mode
## featureScores 3 -none- list
## featureSelected 3 -none- list
## predictions 2693 data.frame list
## accuracy 1 -none- numeric
Compute accuracy for three-way classificationL
# Average accuracy
st <- unique(colData(brca)$STATUS)
acc <- matrix(NA,ncol=length(st),nrow=numSplits)
colnames(acc) <- st
for (k in 1:numSplits) {
pred <- out[[sprintf("Split%i",k)]][["predictions"]];
tmp <- pred[,c("ID","STATUS","TT_STATUS","PRED_CLASS",
sprintf("%s_SCORE",st))]
for (m in 1:length(st)) {
tmp2 <- subset(tmp, STATUS==st[m])
acc[k,m] <- sum(tmp2$PRED==tmp2$STATUS)/nrow(tmp2)
}
}
print(round(acc*100,2))
## Luminal_A Basal-like Luminal_B
## [1,] 46.43 100 35.71
## [2,] 44.83 100 55.00
Also, examine the confusion matrix. We can see that the model perfectly classifies basal tumours, but performs poorly in distinguishing between the two types of luminal tumours.
res <- out$Split1$predictions
print(table(res[,c("STATUS","PRED_CLASS")]))
## PRED_CLASS
## STATUS Basal-like Luminal_A Luminal_B
## Basal-like 14 0 0
## Luminal_A 5 13 10
## Luminal_B 4 5 5
sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=C LC_NUMERIC=C
## [3] LC_TIME=C LC_COLLATE=C
## [5] LC_MONETARY=C 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
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] rhdf5_2.34.0 BiocFileCache_1.14.0
## [3] dbplyr_2.0.0 curatedTCGAData_1.12.0
## [5] MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0
## [7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
## [9] IRanges_2.24.0 S4Vectors_0.28.1
## [11] MatrixGenerics_1.2.0 matrixStats_0.57.0
## [13] netDx_1.2.2 bigmemory_4.5.36
## [15] Biobase_2.50.0 BiocGenerics_0.36.0
##
## loaded via a namespace (and not attached):
## [1] uuid_0.1-4 AnnotationHub_2.22.0
## [3] NMF_0.23.0 plyr_1.8.6
## [5] igraph_1.2.6 RCy3_2.10.2
## [7] lazyeval_0.2.2 splines_4.0.3
## [9] entropy_1.2.1 BiocParallel_1.24.1
## [11] rncl_0.8.4 ggplot2_3.3.2
## [13] gridBase_0.4-7 scater_1.18.3
## [15] digest_0.6.27 htmltools_0.5.0
## [17] foreach_1.5.1 viridis_0.5.1
## [19] magrittr_2.0.1 memoise_1.1.0
## [21] cluster_2.1.0 doParallel_1.0.16
## [23] ROCR_1.0-11 limma_3.46.0
## [25] annotate_1.68.0 R.utils_2.10.1
## [27] prettyunits_1.1.1 colorspace_2.0-0
## [29] blob_1.2.1 rappdirs_0.3.1
## [31] xfun_0.19 dplyr_1.0.2
## [33] crayon_1.3.4 RCurl_1.98-1.2
## [35] bigmemory.sri_0.1.3 graph_1.68.0
## [37] genefilter_1.72.0 phylobase_0.8.10
## [39] survival_3.2-7 iterators_1.0.13
## [41] ape_5.4-1 glue_1.4.2
## [43] registry_0.5-1 gtable_0.3.0
## [45] zlibbioc_1.36.0 XVector_0.30.0
## [47] DelayedArray_0.16.0 BiocSingular_1.6.0
## [49] kernlab_0.9-29 Rhdf5lib_1.12.0
## [51] shape_1.4.5 SingleCellExperiment_1.12.0
## [53] HDF5Array_1.18.0 scales_1.1.1
## [55] DBI_1.1.0 edgeR_3.32.0
## [57] rngtools_1.5 Rcpp_1.0.5
## [59] viridisLite_0.3.0 xtable_1.8-4
## [61] progress_1.2.2 bit_4.0.4
## [63] rsvd_1.0.3 glmnet_4.0-2
## [65] netSmooth_1.10.0 httr_1.4.2
## [67] RColorBrewer_1.1-2 ellipsis_0.3.1
## [69] farver_2.0.3 pkgconfig_2.0.3
## [71] XML_3.99-0.5 R.methodsS3_1.8.1
## [73] scuttle_1.0.3 locfit_1.5-9.4
## [75] RJSONIO_1.3-1.4 labeling_0.4.2
## [77] later_1.1.0.1 howmany_0.3-1
## [79] tidyselect_1.1.0 rlang_0.4.9
## [81] softImpute_1.4 reshape2_1.4.4
## [83] AnnotationDbi_1.52.0 BiocVersion_3.12.0
## [85] munsell_0.5.0 tools_4.0.3
## [87] ExperimentHub_1.16.0 generics_0.1.0
## [89] RSQLite_2.2.1 ade4_1.7-16
## [91] fastmap_1.0.1 evaluate_0.14
## [93] stringr_1.4.0 yaml_2.2.1
## [95] knitr_1.30 bit64_4.0.5
## [97] purrr_0.3.4 nlme_3.1-150
## [99] sparseMatrixStats_1.2.0 mime_0.9
## [101] R.oo_1.24.0 pracma_2.2.9
## [103] xml2_1.3.2 compiler_4.0.3
## [105] interactiveDisplayBase_1.28.0 beeswarm_0.2.3
## [107] curl_4.3 tibble_3.0.4
## [109] RNeXML_2.4.5 stringi_1.5.3
## [111] highr_0.8 RSpectra_0.16-0
## [113] lattice_0.20-41 Matrix_1.2-18
## [115] markdown_1.1 vctrs_0.3.5
## [117] pillar_1.4.7 lifecycle_0.2.0
## [119] rhdf5filters_1.2.0 BiocManager_1.30.10
## [121] combinat_0.0-8 zinbwave_1.12.0
## [123] BiocNeighbors_1.8.2 data.table_1.13.4
## [125] bitops_1.0-6 irlba_2.3.3
## [127] httpuv_1.5.4 R6_2.5.0
## [129] promises_1.1.1 gridExtra_2.3
## [131] vipor_0.4.5 codetools_0.2-18
## [133] MASS_7.3-53 assertthat_0.2.1
## [135] pkgmaker_0.32.2 withr_2.3.0
## [137] GenomeInfoDbData_1.2.4 locfdr_1.1-8
## [139] hms_0.5.3 grid_4.0.3
## [141] beachmat_2.6.2 tidyr_1.1.2
## [143] DelayedMatrixStats_1.12.1 Rtsne_0.15
## [145] shiny_1.5.0 clusterExperiment_2.10.0
## [147] ggbeeswarm_0.6.0