pca_object.R

# Create PCA object for PCAtools package
# select columns of interest
# and pivot wider
measuraments_annotated %>% 
  dplyr::select(
    dplyr::all_of(c("SeqId", "q_norm", "SampleId"))) %>%
  tidyr::pivot_wider(names_from=SeqId, values_from=q_norm) %>%
  dplyr::distinct() -> metrics_df
# retrieve measurement and transpose to matrix
metrics_df %>%
  dplyr::select(-SampleId) %>%
  base::as.matrix() %>%
  base::t() -> matrix
# assign colnames as sampleids
colnames(matrix) <- metrics_df$SampleId 
# create meta data
measuraments_annotated %>%
  dplyr::select(
    dplyr::all_of(
      c(
        "SampleId", "SUBJID", "AGE", "SEX", "PlateId", 
        "timepoint", "ARMCD", "arm.visit", "rash" ))) %>%
  dplyr::distinct() %>%
  base::as.data.frame() -> meta_df
# assign rownames as sample ids
rownames(meta_df) <- meta_df$SampleId
# create pca object
PCAtools::pca(mat = matrix, metadata=meta_df) -> p