make_mxfda function

Make mxFDA class object

Used to create an object of class mxFDA that can be used with the mxfda package for functional data analysis.

make_mxfda(metadata, spatial = NULL, subject_key, sample_key)

Arguments

• metadata: metadata with columns subject_key and sample_key
• spatial: spatial information, either list or df, with column sample_key. Spatial can be empty if inputting data already derived. See add_summary_function() for more details.
• subject_key: column name in Metadata for subject ID
• sample_key: column linking Metadata to Spatial data

Returns

S4 object of class mxFDA

• Metadata: slot of class data.frame that contains sample and subject level information

• Spatial: slot of class data.frame that contains point level information within samples. An example would be cells belonging to TMA cores

• subject_key: slot of class character that corresponds to a column in the Metadata slot that groups samples at a subject level. An example would be "patient_id"

• sample_key: slot of class character that corresponds to a column both in the Metadata and Spatial slots that links samples to characteristics

• univariate_summaries: slot of class list where univariate summary functions calculated on Spatial would be stored

• bivariate_summaries: slot of class list where bivariate summary functions calculated on Spatial would be stored

• multiivariate_summaries: slot of class list where entropy summary functions calculated on Spatial would be stored

• functional_pca: slot of class list where FPCA results are stored

• functional_mpca: slot of class list where MFPCA results are stored

• functional_cox: slot of class list where functional cox model results are stored

• functional_mcox: slot of class list where mixed functional cox model results are stored

• scalar_on_function: slot of class list where functional models are fit to scalar responses

Details

Examples

#select sample metadata
clinical = lung_df %>%
  dplyr::select(image_id, patient_id, patientImage_id,
                gender, age, survival_days, survival_status, stage) %>%
  dplyr::distinct()
#select the spatial information
spatial = lung_df %>%
  dplyr::select(-image_id, -gender, -age, -survival_days, -survival_status, -stage)
sample_id_column = "patientImage_id"
#create the mxFDA object
mxFDAobject = make_mxfda(metadata = clinical,
                         spatial = spatial,
                         subject_key = "patient_id",
                         sample_key = sample_id_column)

Author(s)

Alex Soupir alex.soupir@moffitt.org