## ----options,echo=FALSE----------------------------------------------- options(width=72) ## ----install, eval=FALSE---------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("Discordant") ## ----initialize------------------------------------------------------- library(discordant) ## ----runOutliers, eval=FALSE------------------------------------------ # data(TCGA_Breast_miRNASeq) # mat.filtered <- splitMADOutlier(TCGA_Breast_miRNASeq,filter0 = TRUE, threshold = 4) ## ----createVectors---------------------------------------------------- data(TCGA_GBM_miRNA_microarray) data(TCGA_GBM_transcript_microarray) groups <- c(rep(1,10), rep(2,10)) #Within -Omics wthn_vectors <- createVectors(TCGA_GBM_transcript_microarray, groups = groups) #Between -Omics btwn_vectors <- createVectors(TCGA_GBM_miRNA_microarray, TCGA_GBM_transcript_microarray, groups = groups) ## ----discordant------------------------------------------------------- data(TCGA_GBM_miRNA_microarray) data(TCGA_GBM_transcript_microarray) groups <- c(rep(1,10), rep(2,10)) #Within -omics wthn_vectors <- createVectors(TCGA_GBM_transcript_microarray, groups = groups) wthn_result <- discordantRun(wthn_vectors$v1, wthn_vectors$v2, TCGA_GBM_transcript_microarray) wthn_result$discordPPMatrix[1:4,1:4] head(wthn_result$discordPPVector) wthn_result$classMatrix[1:4,1:4] head(wthn_result$classVector) head(wthn_result$probMatrix) wthn_result$loglik # Between -omics btwn_vectors <- createVectors(TCGA_GBM_miRNA_microarray, TCGA_GBM_transcript_microarray, groups = groups) btwn_result <- discordantRun(btwn_vectors$v1, btwn_vectors$v2, TCGA_GBM_miRNA_microarray, TCGA_GBM_transcript_microarray) btwn_result$discordPPMatrix[1:3,1:3] head(btwn_result$discordPPVector) btwn_result$classMatrix[1:3,1:3] btwn_result$classMatrix[1:3,1:3] head(btwn_result$classVector) head(btwn_result$probMatrix) btwn_result$loglik ## ----microarrays------------------------------------------------------ data(TCGA_GBM_miRNA_microarray) data(TCGA_GBM_transcript_microarray) groups <- c(rep(1,10), rep(2,10)) #Within -Omics wthn_vectors <- createVectors(TCGA_GBM_transcript_microarray, groups = groups) wthn_result <- discordantRun(wthn_vectors$v1, wthn_vectors$v2, TCGA_GBM_transcript_microarray) #Between -Omics btwn_vectors <- createVectors(TCGA_GBM_miRNA_microarray, TCGA_GBM_transcript_microarray, groups = groups) btwn_result <- discordantRun(btwn_vectors$v1, btwn_vectors$v2, TCGA_GBM_miRNA_microarray, TCGA_GBM_transcript_microarray)