junction_load {dasper} | R Documentation

## 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

[Package dasper version 1.0.0 Index]