ccn_queryGRNstatus: Get Query GRN status
In pcahan1/cancerCellNet: CellNet, for cancer

ccn_queryGRNstatus

R Documentation

Get Query GRN status

Description

Get the GRN status of query samples

Usage

ccn_queryGRNstatus(
  expQuery,
  expTrain,
  stTrain,
  dLevel,
  sidCol,
  grn_return,
  trainNorm = NULL,
  classifier_return,
  classWeight = TRUE,
  exprWeight = FALSE,
  prune = TRUE,
  xmax = 1000,
  predSD = FALSE
)

Arguments

`expQuery`	logRanked query expression matrix
`expTrain`	logRanked training expression matrix
`stTrain`	sample table of training expression matrix
`dLevel`	the name of the column with cancer types
`sidCol`	the name of the column with sample IDs
`grn_return`	the grn list that is returned from `ccn_makeGRN`
`trainNorm`	normalization statistics from `ccn_trainNorm`. If you are using pre-calculated normalization statistics please make sure all the parameters are the same for applying to query and calculating normalization
`classifier_return`	the classifier_return list that is returned from `broadClass_train`
`classWeight`	boolean indicating whether to take the importance of the classification into status calculation
`exprWeight`	boolean indicating whether to take the weight of gene expression into status calculation
`prune`	boolean indicating whether to select exclusive genes for processing classification gene importance
`predSD`	a parameter for calculating normalization statistics from training data