## ----echo=FALSE, message=FALSE, include=TRUE---------------------------------- knitr::opts_chunk$set( echo = TRUE, collapse = TRUE, cache = TRUE, fig.show = 'hold') #str(knitr::opts_chunk$get()) ## ----------------------------------------------------------------------------- require(autonomics, quietly = TRUE) object <- read_rnaseq_counts(file = download_data('billing19.rnacounts.txt'), pca = TRUE, fit = 'limma', plot = TRUE) ## ----------------------------------------------------------------------------- basedir <- file.path(tempdir(), 'datasets') dir.create(basedir, showWarnings = FALSE, recursive = TRUE) if (!dir.exists(file.path(basedir, 'GSE161731'))){ GEOquery::getGEOSuppFiles("GSE161731", baseDir=basedir) } object <- read_rnaseq_counts( file = file.path(basedir, 'GSE161731/GSE161731_counts.csv.gz'), sfile = file.path(basedir, 'GSE161731/GSE161731_counts_key.csv.gz'), sfileby = 'rna_id', subgroupvar = 'gender', pca = TRUE, fit = 'limma', plot = TRUE) ## ----------------------------------------------------------------------------- #object <- read_rnaseq_counts( # file = '~/autonomicscache/datasets/GSE161731/GSE161731_counts.csv.gz', # sfile = '~/autonomicscache/datasets/GSE161731/GSE161731_counts_key.csv.gz', # sfileby = 'rna_id', # subgroupvar = 'gender', # block = 'subject_id') ## ----results = 'hide', eval = FALSE------------------------------------------- # # not run to avoid issues with R CMD CHECK # if (requireNamespace('Rsubread')){ # object <- read_rnaseq_bams( # dir = download_data('billing16.bam.zip'), # paired = TRUE, # genome = 'hg38', # pca = TRUE, # fit = 'limma', # plot = TRUE) # } ## ----------------------------------------------------------------------------- file <- download_data('billing19.rnacounts.txt') # log2counts object <- read_rnaseq_counts(file, cpm = FALSE, voom = FALSE, fit = 'limma', verbose = FALSE, plot = FALSE) colSums(summarize_fit(object, 'limma')[, -1]) # log2cpm object <- read_rnaseq_counts(file, cpm = TRUE, voom = FALSE, fit = 'limma', verbose = FALSE, plot=FALSE) colSums(summarize_fit(object, 'limma')[, -1]) # log2cpm + voom object <- read_rnaseq_counts(file, # log2 cpm + voom cpm = TRUE, voom = TRUE, fit = 'limma', verbose = FALSE, plot=FALSE) colSums(summarize_fit(object, 'limma')[, -1]) ## ----------------------------------------------------------------------------- object <- read_proteingroups(file = download_data('fukuda20.proteingroups.txt'), pca = TRUE, fit = 'limma', plot = TRUE) ## ----------------------------------------------------------------------------- object <- read_proteingroups( file = download_data('billing19.proteingroups.txt'), select_subgroups = c('E00_STD', 'E01_STD', 'E02_STD', 'E05_STD', 'E15_STD', 'E30_STD', 'M00_STD'), pca = TRUE, fit = 'limma', plot = TRUE) ## ----------------------------------------------------------------------------- object <- read_phosphosites( file = download_data('billing19.phosphosites.txt'), proteinfile = download_data('billing19.proteingroups.txt'), select_subgroups = c('E00_STD', 'E01_STD', 'E02_STD', 'E05_STD', 'E15_STD', 'E30_STD', 'M00_STD'), pca = TRUE, fit = 'limma', plot = TRUE) ## ----fig.width=7, fig.height=4, out.width="95%"------------------------------- object <- read_metabolon( file = download_data('atkin18.metabolon.xlsx'), subgroupvar = 'SET', pca = TRUE, fit = 'limma', block = 'SUB', plot = TRUE) ## ----------------------------------------------------------------------------- object <- read_somascan( file = download_data('atkin18.somascan.adat'), pca = TRUE, fit = 'limma', block = 'Subject_ID', plot = TRUE) ## ----------------------------------------------------------------------------- sessionInfo()