junction_load: Load junctions from RNA-sequencing data

In dzhang32/dasper: Detecting abberant splicing events from RNA-sequencing data

Load junctions from RNA-sequencing data

Description

junction_load loads in raw patient and control junction data and formats it into a RangedSummarizedExperiment-class object. Control samples can be the user's in-house samples or selected from GTEx v6 data publicly released through the recount2 and downloaded through snaptron. By default, junction_load expects the junction data to be in STAR aligned format (SJ.out) but this can be modified via the argument load_func.

Usage

junction_load(
  junction_paths,
  metadata = dplyr::tibble(samp_id = stringr::str_c("samp_",
    seq_along(junction_paths))),
  controls = rep(FALSE, length(junction_paths)),
  load_func = .STAR_load,
  chrs = NULL,
  coord_system = 1
)

Arguments

junction_paths	path(s) to junction data.
metadata	data.frame containing sample metadata with rows in the same order as junction_paths.
controls	either a logical vector of the same length as junction_paths with TRUE representing controls. Or, one of "fibroblasts", "lymphocytes", "skeletal_muscle", "whole_blood" representing the samples of which GTEx tissue to use as controls. By default, will assume all samples are patients.
load_func	function to load in junctions. By default, requires STAR formatted junctions (SJ.out). But this can be switched dependent on the format of the user's junction data. Function must take as input a junction path then return a data.frame with the columns "chr", "start", "end", "strand" and "count".
chrs	chromosomes to keep. By default, no filter is applied.
coord_system	1 (1-based) or 0 (0-based) denoting the co-ordinate system corresponding to the user junctions from junction_paths. Only used when controls is set to "fibroblasts" to ensure GTEx data is harmonised to match the co-ordinate system of the user's junctions.

Value

RangedSummarizedExperiment-class object containing junction data.

Examples

junctions_example_1_path <-
    system.file("extdata",
        "junctions_example_1.txt",
        package = "dasper",
        mustWork = TRUE
    )
junctions_example_2_path <-
    system.file("extdata",
        "junctions_example_2.txt",
        package = "dasper",
        mustWork = TRUE
    )

junctions <-
    junction_load(
        junction_paths = c(junctions_example_1_path, junctions_example_2_path)
    )

junctions

dzhang32/dasper documentation built on Dec. 14, 2024, 8:33 p.m.