get_bams.RdGet full paths for bam files for a sample or patient.
get_bams(this_sample_id, this_patient_id)Sample ID of interest.
patient ID of interest.
A list that contains the genome_build and an igv-friendly build (igv_build), a list of bam file paths for tumour, normal and mrna data.
Returns a list with BAM paths for tumour, normal and mrna data.
This function expects a sample ID (this_sample_id) or a patient ID (this_patient_id).
#example 1, using a sample ID
bam_details = get_bams(this_sample_id = "HTMCP-01-06-00422-01A-01D")
#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(i = "In argument: `seq_type %in% seq_type_filter & tissue_status == \"normal\"`."), trace = structure(list(call = list(pkgdown::build_reference(lazy = TRUE), purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, examples_env = examples_env, run_dont_run = run_dont_run), map_("list", .x, .f, ..., .progress = .progress), with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)), withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } }), call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i), .f(.x[[i]], ...), withCallingHandlers(data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), error = function(err) { msg <- c(paste0("Failed to parse Rd in ", topic$file_in), i = err$message) abort(msg, parent = err) }), data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), run_examples(tags$tag_examples[[1]], env = if (is.null(examples_env)) NULL else new.env(parent = examples_env), topic = tools::file_path_sans_ext(topic$file_in), run_dont_run = run_dont_run), highlight_examples(code, topic, env = env), downlit::evaluate_and_highlight(code, fig_save = fig_save_topic, env = child_env(env), output_handler = evaluate::new_output_handler(value = pkgdown_print)), evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler), evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing), timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)), try(f, silent = TRUE), tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler), withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), eval_with_user_handlers(expr, envir, enclos, user_handlers), eval(expr, envir, enclos), eval(expr, envir, enclos), get_bams(this_sample_id = "HTMCP-01-06-00422-01A-01D"), get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter), sample_meta %>% dplyr::filter(seq_type %in% seq_type_filter & tissue_status == "normal") %>% dplyr::select(patient_id, sample_id, seq_type, genome_build) %>% as.data.frame() %>% dplyr::rename(normal_sample_id = "sample_id"), dplyr::rename(., normal_sample_id = "sample_id"), as.data.frame(.), dplyr::select(., patient_id, sample_id, seq_type, genome_build), dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter.data.frame(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter_rows(.data, dots, by), filter_eval(dots, mask = mask, error_call = error_call, user_env = user_env), withCallingHandlers(mask$eval_all_filter(dots, env_filter), error = dplyr_error_handler(dots = dots, mask = mask, bullets = filter_bullets, error_call = error_call), warning = function(cnd) { local_error_context(dots, i, mask) warning_handler(cnd) }, `dplyr:::signal_filter_one_column_matrix` = function(e) { warn_filter_one_column_matrix(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_across` = function(e) { warn_filter_across(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_data_frame` = function(e) { warn_filter_data_frame(env = error_call, user_env = user_env) }), mask$eval_all_filter(dots, env_filter), eval(), seq_type %in% seq_type_filter, .handleSimpleError(`<fn>`, "object 'seq_type_filter' not found", base::quote(seq_type %in% seq_type_filter)), h(simpleError(msg, call)), .handleSimpleError(`<fn>`, "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", base::quote(h(simpleError(msg, call)))), h(simpleError(msg, call)), abort(message, class = error_class, parent = parent, call = error_call)), parent = c(0L, 1L, 2L, 3L, 4L, 3L, 3L, 7L, 7L, 9L, 10L, 11L, 12L, 13L, 14L, 14L, 16L, 17L, 18L, 19L, 20L, 14L, 14L, 14L, 24L, 25L, 26L, 27L, 28L, 0L, 0L, 0L, 0L, 0L, 34L, 35L, 36L, 36L, 38L, 0L, 0L, 41L, 0L, 43L, 44L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("pkgdown", "purrr", "purrr", "purrr", "base", "purrr", "pkgdown", "base", "pkgdown", "pkgdown", "pkgdown", "downlit", "evaluate", "evaluate", "evaluate", "evaluate", "base", "base", "base", "base", "base", "base", "base", "evaluate", "base", "base", "GAMBLR", "GAMBLR", NA, "dplyr", "BiocGenerics", "dplyr", "dplyr", "dplyr", "dplyr", "dplyr", "base", NA, "dplyr", NA, "base", "base", "base", "dplyr", "rlang"), scope = c("::", "::", ":::", ":::", "::", ":::", "local", "::", ":::", ":::", ":::", "::", "::", ":::", "local", "local", "::", "::", "local", "local", "local", "::", "::", ":::", "::", "::", "::", "::", NA, "::", "::", "::", "::", ":::", ":::", ":::", "::", NA, "local", NA, "::", "local", "::", "local", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -45L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = structure(list( message = "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", call = h(simpleError(msg, call))), class = c("simpleError", "error", "condition")), rlang = list(inherit = TRUE), call = dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), use_cli_format = TRUE), class = c("rlang_error", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': ℹ In argument: `seq_type %in% seq_type_filter & tissue_status ==
#> "normal"`.
#> Caused by error in `h()`:
#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found
#example 2, using a patient ID
bam_details = get_bams(this_patient_id = "HTMCP-01-06-00422")
#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(i = "In argument: `seq_type %in% seq_type_filter & tissue_status == \"normal\"`."), trace = structure(list(call = list(pkgdown::build_reference(lazy = TRUE), purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, examples_env = examples_env, run_dont_run = run_dont_run), map_("list", .x, .f, ..., .progress = .progress), with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)), withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } }), call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i), .f(.x[[i]], ...), withCallingHandlers(data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), error = function(err) { msg <- c(paste0("Failed to parse Rd in ", topic$file_in), i = err$message) abort(msg, parent = err) }), data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), run_examples(tags$tag_examples[[1]], env = if (is.null(examples_env)) NULL else new.env(parent = examples_env), topic = tools::file_path_sans_ext(topic$file_in), run_dont_run = run_dont_run), highlight_examples(code, topic, env = env), downlit::evaluate_and_highlight(code, fig_save = fig_save_topic, env = child_env(env), output_handler = evaluate::new_output_handler(value = pkgdown_print)), evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler), evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing), timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)), try(f, silent = TRUE), tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler), withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), eval_with_user_handlers(expr, envir, enclos, user_handlers), eval(expr, envir, enclos), eval(expr, envir, enclos), get_bams(this_patient_id = "HTMCP-01-06-00422"), get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter), sample_meta %>% dplyr::filter(seq_type %in% seq_type_filter & tissue_status == "normal") %>% dplyr::select(patient_id, sample_id, seq_type, genome_build) %>% as.data.frame() %>% dplyr::rename(normal_sample_id = "sample_id"), dplyr::rename(., normal_sample_id = "sample_id"), as.data.frame(.), dplyr::select(., patient_id, sample_id, seq_type, genome_build), dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter.data.frame(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter_rows(.data, dots, by), filter_eval(dots, mask = mask, error_call = error_call, user_env = user_env), withCallingHandlers(mask$eval_all_filter(dots, env_filter), error = dplyr_error_handler(dots = dots, mask = mask, bullets = filter_bullets, error_call = error_call), warning = function(cnd) { local_error_context(dots, i, mask) warning_handler(cnd) }, `dplyr:::signal_filter_one_column_matrix` = function(e) { warn_filter_one_column_matrix(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_across` = function(e) { warn_filter_across(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_data_frame` = function(e) { warn_filter_data_frame(env = error_call, user_env = user_env) }), mask$eval_all_filter(dots, env_filter), eval(), seq_type %in% seq_type_filter, .handleSimpleError(`<fn>`, "object 'seq_type_filter' not found", base::quote(get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter))), h(simpleError(msg, call)), .handleSimpleError(`<fn>`, "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", base::quote(h(simpleError(msg, call)))), h(simpleError(msg, call)), abort(message, class = error_class, parent = parent, call = error_call)), parent = c(0L, 1L, 2L, 3L, 4L, 3L, 3L, 7L, 7L, 9L, 10L, 11L, 12L, 13L, 14L, 14L, 16L, 17L, 18L, 19L, 20L, 14L, 14L, 14L, 24L, 25L, 26L, 27L, 28L, 0L, 0L, 0L, 0L, 0L, 34L, 35L, 36L, 36L, 38L, 0L, 0L, 41L, 0L, 43L, 44L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("pkgdown", "purrr", "purrr", "purrr", "base", "purrr", "pkgdown", "base", "pkgdown", "pkgdown", "pkgdown", "downlit", "evaluate", "evaluate", "evaluate", "evaluate", "base", "base", "base", "base", "base", "base", "base", "evaluate", "base", "base", "GAMBLR", "GAMBLR", NA, "dplyr", "BiocGenerics", "dplyr", "dplyr", "dplyr", "dplyr", "dplyr", "base", NA, "dplyr", NA, "base", "base", "base", "dplyr", "rlang"), scope = c("::", "::", ":::", ":::", "::", ":::", "local", "::", ":::", ":::", ":::", "::", "::", ":::", "local", "local", "::", "::", "local", "local", "local", "::", "::", ":::", "::", "::", "::", "::", NA, "::", "::", "::", "::", ":::", ":::", ":::", "::", NA, "local", NA, "::", "local", "::", "local", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -45L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = structure(list( message = "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", call = h(simpleError(msg, call))), class = c("simpleError", "error", "condition")), rlang = list(inherit = TRUE), call = dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), use_cli_format = TRUE), class = c("rlang_error", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': ℹ In argument: `seq_type %in% seq_type_filter & tissue_status ==
#> "normal"`.
#> Caused by error in `h()`:
#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found