signature.prediction.1: logistic regression based signature prediction and cross...

In xu-lab/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

logistic regression based signature prediction and cross cluster validation Cell type specific signature prediction

Usage

signature.prediction.1(ES, group.by = "CLUSTER", groups = NULL,
  trainset.prefix = TRAINSET.PREFIX,
  train.class.prefix = TRAIN.CLASS.PREFIX, testset.prefix = TESTSET.PREFIX,
  test.statistic.metric.prefix = TEST.STATS.METRIC.PREFIX,
  common.prefix = COMMON.PREFIX, unique.prefix = UNIQUE.PREFIX,
  syn.sim.prefix = SYN.SIM.PREFIX, signature.prefix = SIGNATURE.PREFIX,
  gene.symbol.label = GENE.SYMBOL.LABEL, verbose = TRUE, export = TRUE,
  dir.prefix = "")

Arguments

ES	(ExpressionSet) an ExpressionSet object containing the single cell RNA-seq data
group.by	(character) the name of the column that contains the cluster information
groups	(character) the clusters for signature prediction
trainset.prefix	(character) prefix for labeling the columns encoding the training instances for each group
train.class.prefix	(character) prefix for labeling the columns encoding the class of group specific training instances
testset.prefix	(character) prefix for labeling the columns encoding the testing instances for each group
test.statistic.metric.prefix	(character) prefix for labeling the columns encoding the results of test statistic metric for each group
common.prefix	(character) prefix for labeling the columns encoding the results of common metric for each group
unique.prefix	(character) prefix for labeling the columns encoding the results of unique metric for each group
syn.sim.prefix	(character) prefix for labeling the columns encoding the results of synthetic profile similarity metric for each group
signature.prefix	(character) prefix for labeling the columns encoding the results of signature prediction
gene.symbol.label	(character) the name of the column encoding gene symbols
verbose	(logical)
export	(logical) wheterh to export the ExpressionSet
export.components	(character) the components of an ExpressionSet object that will be exported

Value

an ExpressionSet object containing the results of signature prediction in the attributes of fData

xu-lab/SINCERA documentation built on Feb. 3, 2021, 4:19 a.m.