## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("ObMiTi") ## ----------------------------------------------------------------------------- # loading required libraries library(ExperimentHub) library(SummarizedExperiment) ## ----------------------------------------------------------------------------- # query package resources on ExperimentHub eh <- ExperimentHub() query(eh, "ObMiTi") # load data from ExperimentHub ob_counts <- query(eh, "ObMiTi")[[1]] # print object ob_counts ## ----------------------------------------------------------------------------- # print count matrix assay(ob_counts)[1:5, 1:5] ## ----------------------------------------------------------------------------- # View Structure of counts str(colData(ob_counts)) # Studies' metadata available names(colData(ob_counts)) # Sample GSM ID (Same ob_counts$geo_accession) rownames(colData(ob_counts)) # Sample strain, tissue and diet ID ob_counts$title # Frequencies of different diets table(ob_counts$diet.ch1) # Frequncies of tissues table(ob_counts$tissue.ch1) # crosstable of tissue and diet and stratify by genotype table(ob_counts$diet.ch1, ob_counts$tissue.ch1,ob_counts$genotype.ch1) # Summarize Numeric data summary(data.frame(colData(ob_counts))) ## ----------------------------------------------------------------------------- metadata(ob_counts)$measures ## ----------------------------------------------------------------------------- # print GRanges object rowRanges(ob_counts) ## ----------------------------------------------------------------------------- se <- ob_counts[rowRanges(ob_counts)$biotype == 'protein_coding',] ## ----------------------------------------------------------------------------- plot(log(assay(se)[1:100,])) ## ----citation, warning=FALSE, eval=FALSE-------------------------------------- # #citing the package # citation("ObMiTi") ## ----session_info------------------------------------------------------------- devtools::session_info()