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

Description Usage Arguments Value

View source: R/signature.R

Description

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

Usage

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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


minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.