get_salmon_root: Get Salmon root directory

In jmw86069/platjam: Platform Jam, biological platform importers.

Get Salmon root directory

Description

Get Salmon root directory

Usage

get_salmon_root(file, ...)

Arguments

file	character path to a Salmon output file, or a vector of files.
...	additional arguments are ignored.

Details

This function uses the rprojroot package to find the root output directory of a Salmon quant analysis, looking for the file "cmd_info.json". If this file is not found, this function returns NULL.

Value

file path to the Salmon root directory, or NA if the Salmon root directory could not be found.

See Also

Other jam nextgen sequence functions: get_salmon_meta(), parse_salmon_flenfile(), save_salmon_qc_xlsx()

Examples

cmdinfopath <- system.file("data", "salmonOut", "cmd_info.json", package="platjam");
if (nchar(cmdinfopath) > 0) {
   get_salmon_root(cmdinfopath);
}

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.