## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], ISAnalytics = citation("ISAnalytics")[1] ) ## ----echo=FALSE--------------------------------------------------------------- inst_chunk_path <- system.file("rmd", "install_and_options.Rmd", package = "ISAnalytics") ## ----include=FALSE------------------------------------------------------------ knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ISAnalytics") ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # # The following initializes usage of Bioc devel # BiocManager::install(version='devel') # # BiocManager::install("ISAnalytics") ## ----eval=FALSE--------------------------------------------------------------- # if (!require(devtools)) { # install.packages("devtools") # } # devtools::install_github("calabrialab/ISAnalytics", # ref = "RELEASE_3_14", # dependencies = TRUE, # build_vignettes = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!require(devtools)) { # install.packages("devtools") # } # devtools::install_github("calabrialab/ISAnalytics", # ref = "master", # dependencies = TRUE, # build_vignettes = TRUE) ## ----OptVerbose, eval=FALSE--------------------------------------------------- # # DISABLE # options("ISAnalytics.verbose" = FALSE) # # # ENABLE # options("ISAnalytics.verbose" = TRUE) # ## ----OptWidg, eval=FALSE------------------------------------------------------ # # DISABLE HTML REPORTS # options("ISAnalytics.reports" = FALSE) # # # ENABLE HTML REPORTS # options("ISAnalytics.reports" = TRUE) ## ----echo=FALSE--------------------------------------------------------------- library(ISAnalytics) print(default_meta_agg(), width = Inf) ## ----------------------------------------------------------------------------- data("association_file", package = "ISAnalytics") aggregated_meta <- aggregate_metadata(association_file = association_file) ## ----echo=FALSE--------------------------------------------------------------- print(aggregated_meta) ## ----------------------------------------------------------------------------- data("integration_matrices", package = "ISAnalytics") data("association_file", package = "ISAnalytics") aggreg <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(aggreg, width = Inf) ## ----------------------------------------------------------------------------- agg1 <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, key = c("SubjectID", "ProjectID"), value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(agg1, width = Inf) ## ----------------------------------------------------------------------------- agg2 <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, key = "SubjectID", lambda = list(mean = ~ mean(.x, na.rm = TRUE)), value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(agg2, width = Inf) ## ----------------------------------------------------------------------------- agg3 <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, key = "SubjectID", lambda = list(describe = ~ list(psych::describe(.x))), value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(agg3, width = Inf) ## ----------------------------------------------------------------------------- agg4 <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, key = "SubjectID", lambda = list(sum = sum, mean = mean), value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(agg4, width = Inf) ## ----------------------------------------------------------------------------- agg5 <- aggregate_values_by_key( x = integration_matrices, association_file = association_file, key = "SubjectID", lambda = list(sum = sum, mean = mean), group = c(mandatory_IS_vars()), value_cols = c("seqCount", "fragmentEstimate") ) ## ----echo=FALSE--------------------------------------------------------------- print(agg5, width = Inf) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))