## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE, include=TRUE------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("pmp") ## ----message=FALSE, warning=FALSE--------------------------------------------- library(pmp) library(SummarizedExperiment) library(S4Vectors) ## ----eval=FALSE--------------------------------------------------------------- # help ("MTBLS79") ## ----------------------------------------------------------------------------- data(MTBLS79) MTBLS79 ## ----------------------------------------------------------------------------- sum(is.na(assay(MTBLS79))) sum(is.na(assay(MTBLS79))) / length(assay(MTBLS79)) * 100 ## ----------------------------------------------------------------------------- MTBLS79_filtered <- filter_samples_by_mv(df=MTBLS79, max_perc_mv=0.1) MTBLS79_filtered sum(is.na(assay(MTBLS79_filtered))) ## ----------------------------------------------------------------------------- MTBLS79_filtered <- filter_peaks_by_fraction(df=MTBLS79_filtered, min_frac=0.9, classes=MTBLS79_filtered$Class, method="QC", qc_label="QC") MTBLS79_filtered sum(is.na(assay(MTBLS79_filtered))) ## ----------------------------------------------------------------------------- MTBLS79_filtered <- filter_peaks_by_fraction(df=MTBLS79_filtered, min_frac=0.9, classes=MTBLS79_filtered$Class, method="across") MTBLS79_filtered sum(is.na(assay(MTBLS79_filtered))) ## ----------------------------------------------------------------------------- MTBLS79_filtered <- filter_peaks_by_rsd(df=MTBLS79_filtered, max_rsd=30, classes=MTBLS79_filtered$Class, qc_label="QC") MTBLS79_filtered sum(is.na(assay(MTBLS79_filtered))) ## ----------------------------------------------------------------------------- processing_history(MTBLS79_filtered) ## ----------------------------------------------------------------------------- MTBLS79_pqn_normalised <- pqn_normalisation(df=MTBLS79_filtered, classes=MTBLS79_filtered$Class, qc_label="QC") ## ----------------------------------------------------------------------------- MTBLS79_mv_imputed <- mv_imputation(df=MTBLS79_pqn_normalised, method="knn") ## ----------------------------------------------------------------------------- MTBLS79_glog <- glog_transformation(df=MTBLS79_mv_imputed, classes=MTBLS79_filtered$Class, qc_label="QC") ## ----plot_glog, fig.width=5--------------------------------------------------- opt_lambda <- processing_history(MTBLS79_glog)$glog_transformation$lambda_opt glog_plot_optimised_lambda(df=MTBLS79_mv_imputed, optimised_lambda=opt_lambda, classes=MTBLS79_filtered$Class, qc_label="QC") ## ----------------------------------------------------------------------------- peak_matrix <- t(assay(MTBLS79)) sample_classes <- MTBLS79$Class class(peak_matrix) dim(peak_matrix) class(sample_classes) ## ----message=TRUE, warning=TRUE----------------------------------------------- mv_imputed <- mv_imputation(df=peak_matrix, method="mn") rsd_filtered <- filter_peaks_by_rsd(df=mv_imputed, max_rsd=30, classes=sample_classes, qc_label="QC") class (mv_imputed) dim (mv_imputed) class (rsd_filtered) dim (rsd_filtered) ## ----------------------------------------------------------------------------- sessionInfo()