# prepare a data set to be used below
data_path <- 'ellahi'
sample_ids <- grep('^SR', dir(data_path), value = TRUE)
sample_ids <- rev(sample_ids)
target_mapping <- read.table(file.path(data_path, 'target_mappings.txt'), header = TRUE,
stringsAsFactors = FALSE, sep="\t", quote="")
incomplete_mapping <- read.table(file.path(data_path, 'target_mappings_incomplete.txt'), header = TRUE,
stringsAsFactors = FALSE, sep="\t", quote="")
small_study_map <- data.frame(sample = "small_sample", condition = "test",
path = "small_test_data/kallisto.N",
stringsAsFactors = F)
small_target_mapping <- read.table('small_test_data/target_mapping.txt', header = TRUE,
stringsAsFactors = FALSE, sep="\t", quote="")
study_mapping <- read.table(file.path(data_path, 'study_design.txt'), header = TRUE,
stringsAsFactors = FALSE)
study_mapping <- dplyr::select(study_mapping, sample = run, condition)
stopifnot(sample_ids == study_mapping$sample)
result_paths <- file.path(data_path, sample_ids, 'kallisto')
study_mapping <- dplyr::mutate(study_mapping, path = result_paths)
study_formula <- ~condition
trans_test_data <- sleuth_load(file.path(data_path, 'ellahi_transcript.rda'))
gene_test_data <- sleuth_load(file.path(data_path, 'ellahi_gene.rda'))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.