This is is the main function in v0 of verywise.
It checks the user inputs and runs the single_lmm function across all vertices.
Usage
run_vw_lmm(
formula,
pheno,
subj_dir,
outp_dir = NULL,
hemi = c("both", "lh", "rh"),
seed = 3108,
n_cores = 1,
FS_HOME = Sys.getenv("FREESURFER_HOME"),
folder_id = "folder_id",
verbose = TRUE,
...
)Arguments
- formula
: model formula object (this should specify a LME model)
- pheno
: the phenotype data object (already loaded in the global environment) or a string containing a file path. Supported file extensions are: rds, csv, txt and sav.
- subj_dir
: path to the FreeSurfer data, this expects a verywise structure.
- outp_dir
: output path, where do you want results to be stored. If none is provided by the user, a "results" sub-directory will be created inside
subj_dir.- hemi
: (default = "both") which hemispheres to run.
- seed
: (default = 3108) random seed.
- n_cores
: (default = 1) number of cores for parallel processing.
- FS_HOME
: FreeSurfer directory, i.e.
$FREESURFER_HOME.- folder_id
: (default = "folder_id") the name of the column in pheno that contains the directory names of the input neuroimaging data (e.g. "sub-10_ses-T1").
- verbose
: (default = TRUE)
- ...
Arguments passed on to
hemi_vw_lmmmeasure: (default =
gsub("vw_", "", all.vars(formula)[1])) vertex-wise measure this should be the same as specified in formulafwhm: (default = 10) full-width half maximum value
target: (default = "fsaverage") template on which to register vertex-wise data.
model: (default =
"lme4::lmer") # "stats::lm"