## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(dpi = 300) knitr::opts_chunk$set(cache=FALSE) ## ----echo = FALSE, hide=TRUE, message=FALSE, warning=FALSE-------------------- library('oppti') ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("oppti") ## ----eval = FALSE------------------------------------------------------------- # browseVignettes("oppti") ## ----eval = TRUE-------------------------------------------------------------- set.seed(1) cohort1.proteomes = as.data.frame(matrix(abs(rnorm(100*30)), 100, 30)) rownames(cohort1.proteomes) = paste('marker', 1:100, sep = '') colnames(cohort1.proteomes) = paste('cohort1.sample', 1:30, sep = '') ## ----eval = TRUE-------------------------------------------------------------- library('oppti') result = oppti(cohort1.proteomes) ## ----eval = TRUE-------------------------------------------------------------- cohort1.outlier.scores = result[[1]] ## ----eval = TRUE, echo = FALSE, size = 8-------------------------------------- knitr::kable(cohort1.outlier.scores[[1]][1:10,1:4], digits = 2, caption = "Example matrix of the outlier scores, displayed for the first 10 proteins (rows) and the first 4 samples (columns)", row.names = TRUE) ## ----eval = TRUE-------------------------------------------------------------- cohort1.normal.states = result[[2]] ## ----eval = TRUE, echo = FALSE, size = 8-------------------------------------- knitr::kable(cohort1.normal.states[[1]][1:10,1:4], digits = 2, caption = "Example matrix of the normal states", row.names = TRUE) ## ----eval = TRUE-------------------------------------------------------------- cohort1.markers.tests = result[[3]] ## ----eval = TRUE, echo = FALSE, size = 8-------------------------------------- knitr::kable(cohort1.markers.tests[[1]][1:10,], digits = 4, caption = "Statistical significance of outlying markers", row.names = TRUE) ## ----eval = TRUE-------------------------------------------------------------- cohort2.proteomes = as.data.frame(matrix(abs(rnorm(80*20)), 80, 20)) rownames(cohort2.proteomes) = paste('marker', 51:130, sep = '') colnames(cohort2.proteomes) = paste('cohort2.sample', 31:50, sep = '') ## ----eval = TRUE-------------------------------------------------------------- result = oppti(list(cohort1.proteomes,cohort2.proteomes)) ## ----eval = TRUE-------------------------------------------------------------- outlier.scores = result[[1]] ## ----eval = TRUE-------------------------------------------------------------- cohort1.outlier.scores = outlier.scores[[1]] ## ----eval = TRUE, echo = FALSE, size = 8-------------------------------------- knitr::kable(cohort1.outlier.scores[1:10,1:4], digits = 2, caption = "Example outlier scores in cohort1", row.names = TRUE) ## ----eval = TRUE-------------------------------------------------------------- cohort2.outlier.scores = outlier.scores[[2]] ## ----eval = TRUE, echo = FALSE, size = 8-------------------------------------- knitr::kable(cohort2.outlier.scores[1:10,1:4], digits = 2, caption = "Example outlier scores in cohort2", row.names = TRUE) ## ----eval = FALSE------------------------------------------------------------- # result = oppti(list(cohort1.proteomes,cohort2.proteomes), draw.sc.plots = TRUE, # panel.markers = rownames(cohort1.proteomes)[46:55]) ## ----eval = FALSE------------------------------------------------------------- # result = oppti(list(cohort1.proteomes,cohort2.proteomes), draw.ou.plots = TRUE, # panel.markers = rownames(cohort1.proteomes)[46:55]) ## ----eval = FALSE------------------------------------------------------------- # result = oppti(list(cohort1.proteomes,cohort2.proteomes), # draw.ou.markers = c('marker50', 'marker55'), # panel.markers = rownames(cohort1.proteomes)[46:55])