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run EpiDISH

Source: R/epidish.R
run_epidish.Rd

run EpiDISH

Usage

run_epidish(
  methyl_set,
  mode = c("RPC", "CBS", "CP"),
  reference = c("blood", "breast", "epithelial"),
  maxit = 50,
  nu.v = c(0.25, 0.5, 0.7),
  constraint = c("inequality", "equality")
)

Arguments

methyl_set

A minfi MethylSet

mode

Choice of a reference-based method ('RPC','CBS','CP')

reference

A matrix of reference 'centroids', i.e. representative molecular profiles, for a number of cell subtypes. rows label molecular features (e.g. CpGs,...) and columns label the cell-type. IDs need to be provided as rownames and colnames, respectively. Missing value is not allowed, and all values in this matrix should be positive or zero. For DNAm data, values should be beta-values.

maxit

Only used in RPC mode, the limit of the number of IWLS iterations

nu.v

Only used in CBS mode. It is a vector of several candidate nu values. nu is parameter needed for nu-classification, nu-regression, and one-classification in svm. The best estimation results among all candidate nu will be automatically returned.

constraint

Only used in CP mode, you can choose either of 'inequality' or 'equality' normalization constraint. The default is 'inequality' (i.e sum of weights adds to a number less or equal than 1), which was implemented in Houseman et al (2012).

Value

CP-mode A list with the following entries: estF: a matrix of the estimated fractions; ref: the reference centroid matrix used; dataREF: the subset of the input data matrix with only the probes defined in the reference matrix.

CBS-mode A list with the following entries: estF: a matrix of the estimated fractions; nu: a vector of 'best' nu-parameter for each sample; ref: the reference centroid matrix used; dataREF: the subset of the input data matrix with only the probes defined in the reference matrix.

RPC-mode A list with the following entries: estF: a matrix of the estimated fractions; ref: the reference centroid matrix used; dataREF: the subset of the input data matrix with only the probes defined in the reference matrix.