## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png", message = FALSE, error = FALSE, warning = FALSE) BiocStyle::markdown() library(knitr) library(deconvR) library(doParallel) library(dplyr) cl <- parallel::makeCluster(2) doParallel::registerDoParallel(cl) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("deconvR") ## ----message = FALSE, output.lines=10----------------------------------------- library(deconvR) data("HumanCellTypeMethAtlas") head(HumanCellTypeMethAtlas[,1:5]) ## ----message = FALSE, output.lines=10----------------------------------------- data("IlluminaMethEpicB5ProbeIDs") head(IlluminaMethEpicB5ProbeIDs) ## ----message = FALSE, output.lines=10----------------------------------------- samples <- simulateCellMix(3,reference = HumanCellTypeMethAtlas)$simulated head(samples) ## ----message = FALSE, output.lines=10----------------------------------------- sampleMeta <- data.table("Experiment_accession" = colnames(samples)[-1], "Biosample_term_name" = "new cell type") head(sampleMeta) ## ----output.lines=10---------------------------------------------------------- extended_matrix <- findSignatures(samples = samples, sampleMeta = sampleMeta, atlas = HumanCellTypeMethAtlas, IDs = "IDs") head(extended_matrix) ## ----message = FALSE, output.lines=10----------------------------------------- load(system.file("extdata", "WGBS_GRanges.rda", package = "deconvR")) head(WGBS_GRanges) ## ----message = FALSE, output.lines=10----------------------------------------- head(methylKit::methRead(system.file("extdata", "test1.myCpG.txt", package = "methylKit"), sample.id="test", assembly="hg18", treatment=1, context="CpG", mincov = 0)) ## ----message = FALSE, output.lines=10----------------------------------------- data("IlluminaMethEpicB5ProbeIDs") head(IlluminaMethEpicB5ProbeIDs) ## ----output.lines=10---------------------------------------------------------- mapped_WGBS_data <- BSmeth2Probe(probe_id_locations = IlluminaMethEpicB5ProbeIDs, WGBS_data = WGBS_GRanges, multipleMapping = TRUE, cutoff = 10) head(mapped_WGBS_data) ## ----------------------------------------------------------------------------- deconvolution <- deconvolute(reference = HumanCellTypeMethAtlas, bulk = mapped_WGBS_data) deconvolution$proportions ## ----output.lines=10---------------------------------------------------------- data("HumanCellTypeMethAtlas") exampleSamples <- simulateCellMix(1,reference = HumanCellTypeMethAtlas)$simulated exampleMeta <- data.table("Experiment_accession" = "example_sample", "Biosample_term_name" = "example_cell_type") colnames(exampleSamples) <- c("CpGs", "example_sample") colnames(HumanCellTypeMethAtlas)[1] <- c("CpGs") signatures <- findSignatures( samples = exampleSamples, sampleMeta = exampleMeta, atlas = HumanCellTypeMethAtlas, IDs = "CpGs", K = 100, tissueSpecCpGs = TRUE) print(head(signatures[[2]])) ## ----output.lines=10---------------------------------------------------------- data("HumanCellTypeMethAtlas") exampleSamples <- simulateCellMix(1,reference = HumanCellTypeMethAtlas)$simulated exampleMeta <- data.table("Experiment_accession" = "example_sample", "Biosample_term_name" = "example_cell_type") colnames(exampleSamples) <- c("CpGs", "example_sample") colnames(HumanCellTypeMethAtlas)[1] <- c("CpGs") signatures <- findSignatures( samples = exampleSamples, sampleMeta = exampleMeta, atlas = HumanCellTypeMethAtlas, IDs = "CpGs", tissueSpecDMPs = TRUE) print(head(signatures[[2]])) ## ----------------------------------------------------------------------------- sessionInfo() stopCluster(cl)