spatialTIME: create_mif – R documentation

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create_mif

Create Multiplex Immunoflourescent object

Creates an MIF object for use in spatialIF functions

create_mif(
  clinical_data,
  sample_data,
  spatial_list = NULL,
  patient_id = "patient_id",
  sample_id = "image_tag",
  clean_columns = FALSE
)

`clinical_data`	A data frame containing patient level data with one row per participant.
`sample_data`	A data frame containing sample level data with one row per sample. Should at a minimum contain a 2 columns: one for sample names and one for the corresponding patient name.
`spatial_list`	A named list of data frames with the spatial data from each sample making up each individual data frame
`patient_id`	A character string indicating the column name for patient id in sample and clinical data frames.
`sample_id`	A character string indicating the column name for sample id in the sample data frame
`clean_columns`	A logical value indicating if names in spatial data frames should be rewritten in a cleaner format. Default is FALSE.

Returns a custom MIF

`clinical`	Data frame of clinical data
`sample`	Data frame of sample data
`spatial`	Named list of spatial data
`derived`	List of data derived using the MIF object

Spatial Analysis of Vectra Immunoflourescent Data

v1.0.0

MIT + file LICENSE

Authors

Jordan Creed [aut], Ram Thapa [aut], Christopher Wilson [aut], Brooke Fridley [cph], Fridley Lab [cre]

Initial release