Map files to assay types — map

Specify which files correspond to which statistical assays (beta, se, var, t). This mapping is used by as_gds.image_catalog() to construct the GDS.

Usage

map_assays(catalog, ...)

Arguments

catalog

An image_catalog object.

...

Named arguments where names are assay types and values are either:

A regex pattern to match against filenames, OR
A named list like list(column = value) for exact column matching

Value

Updated image_catalog with assay_map.

Examples

# Build a tiny study tree with empty placeholder files
root <- tempfile("study_")
for (s in c("01", "02")) {
  d <- file.path(root, paste0("sub-", s))
  dir.create(d, recursive = TRUE)
  invisible(file.create(file.path(d, c("cope1.nii.gz", "varcope1.nii.gz"))))
}
catalog <- image_catalog(root, "sub-*/*.nii.gz",
                         path_regex = "sub-(?<subject>[^/]+)")

# By filename pattern (regex matched against basenames)
catalog <- map_assays(catalog,
  beta = "^cope[0-9]+\\.nii",
  var = "^varcope[0-9]+\\.nii"
)

# By metadata column value
catalog <- assign_meta(catalog, "stat_type", "^([a-z]+)[0-9]+")
catalog <- map_assays(catalog,
  beta = list(stat_type = "cope"),
  var = list(stat_type = "varcope")
)
summary(catalog)
#> Image Catalog Summary
#> =====================
#> Total files: 4
#> Root directory: /tmp/Rtmp17Odxi/study_1cec7b1afb8f
#> Discovery pattern: sub-*/*.nii.gz
#> 
#> Metadata columns:
#>   basename: 2 unique
#>   subject: 2 unique
#>   stat_type: 2 unique
#> 
#> Assay mappings:
#>   beta: stat_type == 'cope'
#>   var: stat_type == 'varcope'

unlink(root, recursive = TRUE)