## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("delocal") ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("devtools")) { # install.packages("devtools") # } # devtools::install_github("dasroy/delocal") ## ----example,message=FALSE,warning=FALSE-------------------------------------- library(DELocal) count_matrix <- as.matrix(read.table(file = system.file("extdata", "tooth_RNASeq_counts.txt", package = "DELocal"))) colData <- data.frame(condition=gsub("\\..*",x=colnames(count_matrix), replacement = "")) ## ----message=FALSE,warning=FALSE---------------------------------------------- gene_location <- read.table(file = system.file("extdata", "gene_location.txt", package = "DELocal")) head(gene_location) ## ----eval=TRUE---------------------------------------------------------------- library(biomaRt) gene_attributes <- c("ensembl_gene_id", "start_position", "chromosome_name") ensembl_ms_mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org") gene_location_sample <- getBM(attributes=gene_attributes, mart=ensembl_ms_mart, verbose = FALSE) rownames(gene_location_sample) <- gene_location_sample$ensembl_gene_id ## ----message=FALSE,warning=FALSE,error=FALSE---------------------------------- library(SummarizedExperiment) smrExpt <- SummarizedExperiment(assays=list(counts=count_matrix), rowData = gene_location, colData=colData) smrExpt ## ----message=FALSE,warning=FALSE,error=FALSE---------------------------------- library(dplyr) x_genes <- SummarizedExperiment::rowData(smrExpt) %>% as.data.frame() %>% filter(chromosome_name=="X") %>% rownames() DELocal_result <- DELocal(pSmrExpt = smrExpt[x_genes,], nearest_neighbours = 5,pDesign = ~ condition, pValue_cut = 0.05) head(round(DELocal_result,digits = 9)) ## ----message=FALSE,warning=FALSE,error=FALSE---------------------------------- DELocal::plotNeighbourhood(pSmrExpt = smrExpt, pGene_id = "ENSMUSG00000059401", pNearest_neighbours=5, pDesign = ~ condition)$plot ## ----message=FALSE,warning=FALSE,error=FALSE---------------------------------- gene_location_dynamicNeighbourhood <- read.csv(system.file("extdata", "Mouse_TAD_boundaries.csv", package = "DELocal")) rownames(gene_location_dynamicNeighbourhood) <- gene_location_dynamicNeighbourhood$ensembl_gene_id # rename the columns as required by DELocal colnames(gene_location_dynamicNeighbourhood)[4:5] <- c("neighbors_start", "neighbors_end") common_genes <- intersect(rownames(count_matrix), rownames(gene_location_dynamicNeighbourhood) ) smrExpt_dynamicNeighbour <- SummarizedExperiment::SummarizedExperiment( assays = list(counts = count_matrix[common_genes,]), rowData = gene_location_dynamicNeighbourhood[common_genes, ], colData = colData ) ## Selecting only chromosome 1 genes to reduce the runtime # one_genes <- SummarizedExperiment::rowData(smrExpt_dynamicNeighbour) %>% # as.data.frame() %>% # filter(chromosome_name=="1") %>% rownames() DELocal_result_tad <- DELocal(pSmrExpt = smrExpt_dynamicNeighbour[x_genes,], nearest_neighbours = 5,pDesign = ~ condition, pValue_cut = 0.05, pLogFold_cut = 0) head(DELocal_result_tad) ## ----echo=FALSE--------------------------------------------------------------- sessionInfo()