PhiSpace using a single reference

PhiSpaceR_1ref(
  reference,
  query,
  phenotypes = NULL,
  response = NULL,
  refAssay = "log1p",
  queryAssay = NULL,
  regMethod = c("PLS", "PCA"),
  ncomp = NULL,
  nfeat = NULL,
  selectedFeat = NULL,
  center = TRUE,
  scale = FALSE,
  DRinfo = FALSE
)

Arguments

reference: SCE. The reference.
query: SCE or a list of SCE. The query.
phenotypes: Charater. Which types of phenotypes to predict. If NULL, then have to specify response. Currently only support categorical phenotypes. For continuous ones, specify response directly.
response: Named matrix. Rows correspond to cells (columns) in reference; columns correspond to phenotypes. If not NULL, then will override phenotypes. Can be continuous values such as age and BMI.
refAssay: Character. Which assay in reference to use to train PhiSpace
queryAssay: Character. Which assay in query to use for prediction; by default same as refAssay
regMethod: Character. Regression method: one of PLS and PCA
ncomp: Integer.
nfeat: Integer.
selectedFeat: Character.
center: Logic.
scale: Logic.
DRinfo: Logic. Whether to return dimension reduction information from PCA or PLS. Disable to save memory.

Value

A list