Get Salmon root directory
get_salmon_root(file, ...)character path to a Salmon output file, or a vector of files.
additional arguments are ignored.
file path to the Salmon root directory, or NA if
the Salmon root directory could not be found.
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.
Other jam nextgen sequence functions:
get_salmon_meta(),
parse_salmon_flenfile(),
save_salmon_qc_xlsx()
cmdinfopath <- system.file("data", "salmonOut", "cmd_info.json", package="platjam");
if (nchar(cmdinfopath) > 0) {
get_salmon_root(cmdinfopath);
}
#> [1] "/private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmp7zZ5c6/temp_libpath123f74b32cd37/platjam/data/salmonOut"