get_exons {ODER} | R Documentation

## Obtain set of non-overlapping exons

### Description

Downloads a well-defined set of exons to be used in obtaining the optimum set of Expressed regions. These exons are used in calculating the exon deltas.

Calculates the median exon delta and the number of ERs with an exon delta of 0 by comparing each combination of MCC and MRG with the optimum exons from the ensembl database.

Uses a delta calculating function and a well defined set of exons to find which combination of MCC and MRG gives the best definition of the Expressed regions.

### Usage

    get_exons(gtf, ucsc_chr, ignore.strand = TRUE, biotype = "Non-overlapping")

    get_ers_delta(ers, opt_exons, delta_fun = NULL)

    get_opt_ers(ers, ers_delta)

### Arguments

`gtf` | Either a string containg the path to a .gtf file or a pre-imported gtf using `rtracklayer::import` .
`ucsc_chr` | logical scalar, determining whether to add "chr" prefix to the seqnames of non-overlapping exons and change "chrMT" -> "chrM". Note, if set to TRUE and seqnames already have "chr", it will not add another.
`ignore.strand` | logical value for input into `findOverlaps`, default is True.
`biotype` | Filters the GTF file passed in to what would be considered the "Gold Standard" exons. The Default is "Non-overlapping" but the options are: "Non-overlapping" (exons that don't intersect each other), "Three Prime" (3' UTR), "Five Prime" (5' UTR), "Internal" (Internal coding), "lncRNA" (Long Non-Coding RNA), "ncRNA" (Non-Coding RNA) and "Pseudogene"
`ers` | Sets of ERs across various MCCs/MRGs - output of `get_ers`.
`opt_exons` | GRanges object that contains the regions that ideally, you want the ER definitions to match - output of `get_exons`.
`delta_fun` | Function that calculates the delta between ERs and `opt_exons`. Takes as input a set of ERs from `ers` and `opt_exons`. Then outputs a tibble/dataframe containing the summarised delta scores for that set of one set of ERs.
`ers_delta` | tibble/dataframe containing summarised delta values. One row per set of ERs.

### Value

GRanges object containing non-overlapping exons.

tibble/dataframe containing summarised delta values. One row per set of ERs.

list containing optimised ERs, optimal pair of MCC/MRGs and `delta_df`

### Functions

- `get_exons`: Filter for the exons to calculate the deltas against

- `get_ers_delta`: Method to get ers delta to help determine the optimum ers

### Examples

    gtf_url <- paste0(
        "http://ftp.ensembl.org/pub/release-103/gtf/",
        "homo_sapiens/Homo_sapiens.GRCh38.103.chr.gtf.gz"
    )
    gtf_path <- file_cache(gtf_url)

    gtf_gr <- rtracklayer::import(gtf_path)

    eg_opt_exons <- get_exons(
        gtf = gtf_gr,
        ucsc_chr = TRUE,
        ignore.strand = TRUE
    )

    eg_opt_exons
    data(gtex_SRP012682_SRX222703_lung_ers_1, package = "ODER")

    eg_ers_delta <- get_ers_delta(
        ers = gtex_SRP012682_SRX222703_lung_ers_1,
        opt_exons = eg_opt_exons
    )

    eg_ers_delta
    data(gtex_SRP012682_SRX222703_lung_ers_1, package = "ODER")
    opt_ers <- get_opt_ers(
        ers = gtex_SRP012682_SRX222703_lung_ers_1,
        ers_delta = eg_ers_delta
    )
    opt_ers

[Package ODER version 1.0.0 Index]