## ----style, echo = FALSE, results = 'asis', eval=TRUE------------------------- BiocStyle::markdown() options(width = 80, max.print = 1000) knitr::opts_chunk$set( eval = as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache = as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), tidy.opts = list(width.cutoff = 80), tidy = TRUE ) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE, eval=TRUE------------- suppressPackageStartupMessages({ library(systemPipeTools) library(systemPipeR) }) ## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("systemPipeTools") # BiocManager::install("systemPipeR") ## ----documentation, eval=FALSE------------------------------------------------ # library("systemPipeTools") # Loads the package # library(help = "systemPipeTools") # Lists package info # vignette("systemPipeTools") # Opens vignette ## ----targets_counts, eval=TRUE------------------------------------------------ ## Targets file targetspath <- system.file("extdata", "targets.txt", package = "systemPipeR") targets <- read.delim(targetspath, comment = "#") cmp <- systemPipeR::readComp(file = targetspath, format = "matrix", delim = "-") ## Count table file countMatrixPath <- system.file("extdata", "countDFeByg.xls", package = "systemPipeR") countMatrix <- read.delim(countMatrixPath, row.names = 1) showDT(countMatrix) ## ----exploreDDS, eval=TRUE, warning=FALSE------------------------------------- exploredds <- exploreDDS(countMatrix, targets, cmp = cmp[[1]], preFilter = NULL, transformationMethod = "rlog") exploredds ## ----exploreDDSplot, eval=FALSE, warning=FALSE, message=FALSE----------------- # exploreDDSplot(countMatrix, targets, cmp = cmp[[1]], preFilter = NULL, # samples = c("M12A", "M12A", "A12A", "A12A"), # scattermatrix = TRUE) ## ----hclustplot, eval=TRUE---------------------------------------------------- hclustplot(exploredds, method = "spearman") ## ----heatMaplot_samples, eval=TRUE-------------------------------------------- ## Samples plot heatMaplot(exploredds, clust = "samples", plotly = FALSE) ## ----heatMaplot_DEG, eval=TRUE, warning=FALSE--------------------------------- ## Individuals genes identified in DEG analysis ### DEG analysis with `systemPipeR` degseqDF <- systemPipeR::run_DESeq2(countDF = countMatrix, targets = targets, cmp = cmp[[1]], independent = FALSE) DEG_list <- systemPipeR::filterDEGs(degDF = degseqDF, filter = c(Fold = 2, FDR = 10)) ### Plot heatMaplot(exploredds, clust = "ind", DEGlist = unique(as.character(unlist(DEG_list[[1]])))) ## ----PCAplot, eval=TRUE------------------------------------------------------- PCAplot(exploredds, plotly = FALSE) ## ----MDSplot, eval=TRUE------------------------------------------------------- MDSplot(exploredds, plotly = FALSE) ## ----GLMplot, eval=TRUE, warning=FALSE, message=FALSE------------------------- exploredds_r <- exploreDDS(countMatrix, targets, cmp = cmp[[1]], preFilter = NULL, transformationMethod = "raw") GLMplot(exploredds_r, plotly = FALSE) ## ----MAplot, eval=TRUE-------------------------------------------------------- MAplot(degseqDF, comparison = "M12-A12", filter = c(Fold = 1, FDR = 20), genes = "ATCG00280") ## ----tSNEplot, eval=TRUE------------------------------------------------------ tSNEplot(countMatrix, targets, perplexity = 5) ## ----volcanoplot, eval=TRUE--------------------------------------------------- volcanoplot(degseqDF, comparison = "M12-A12", filter = c(Fold = 1, FDR = 20), genes = "ATCG00280") ## ----sessionInfo, eval=TRUE--------------------------------------------------- sessionInfo()