read_junction_table: Read a junction TSV file created by Megadepth as a table

In LieberInstitute/megadepth: megadepth: BigWig and BAM related utilities

Read a junction TSV file created by Megadepth as a table

Description

Read an ⁠*all_jxs.tsv⁠ or ⁠*jxs.tsv⁠ file created by bam_to_junctions() or manually by the user using Megadepth. The rows of a ⁠*jxs.tsv⁠ can have either 7 or 14 columns, which can lead to warnings when reading in - these are safe to ignore. For details on the format of the input TSV file, check https://github.com/ChristopherWilks/megadepth#junctions.

Usage

read_junction_table(tsv_file)

Arguments

tsv_file

A character(1) specifying the path to the tab-separated (TSV) file created manually using megadepth_shell() or on a previous bam_to_junctions() run.

Value

A tibble::tibble() with the junction data that follows the format specified at https://github.com/ChristopherWilks/megadepth#junctions.

Examples

## Install if necessary
install_megadepth()

## Find the example BAM file
example_bam <- system.file("tests", "test.bam",
    package = "megadepth", mustWork = TRUE
)

## Run bam_to_junctions()
example_jxs <- bam_to_junctions(example_bam, overwrite = TRUE)

## Read the junctions in as a tibble
all_jxs <- read_junction_table(example_jxs[["all_jxs.tsv"]])

all_jxs

LieberInstitute/megadepth documentation built on Dec. 14, 2024, 3:30 p.m.