ccn_tfScores: calculate TF scores
In pcahan1/cancerCellNet: CellNet, for cancer

ccn_tfScores

R Documentation

calculate TF scores

Description

calculate the TF that one should target to yield target cell type

Usage

ccn_tfScores(
  expQuery,
  subnetName,
  grnAll,
  trainNorm,
  classifier_return,
  classWeight = TRUE,
  classWeightVal = 3,
  exprWeight = FALSE,
  exprWeightVal = 3,
  correlationFactor = 1,
  prune = TRUE,
  normTFscore = FALSE
)

Arguments

`expQuery`	the logRanked expression matrix for query data
`subnetName`	the name of the target cell type
`grnAll`	result of running `ccn_makeGRN`
`trainNorm`	result of running `ccn_trainNorm`
`classifier_return`	the classifier_return list that is returned from `broadClass_train`
`classWeight`	whether to take the weight of the classifier into calculation
`classWeightVal`	the value of the classifier weight
`exprWeight`	whether to take the weight of the expression into calculation
`exprWeightVal`	the value of the expression weight
`correlationFactor`	the weight of correlation direction in the network
`prune`	the pararmeter for pruning importance of gene pairs
`normTFscore`	boolean indicate whether to normalize TF scores