sigpred.training.sets: Constructing group specific training sets for signature...

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

Description

Constructing group specific training sets for signature prediction

Usage

sigpred.training.sets(ES, group.by = CLUSTER.LABEL, groups = NULL,
  trainset.prefix = TRAINSET.PREFIX,
  train.class.prefix = TRAIN.CLASS.PREFIX,
  test.statistic.metric.prefix = TEST.STATS.METRIC.PREFIX,
  common.prefix = COMMON.PREFIX, unique.prefix = UNIQUE.PREFIX,
  syn.sim.prefix = SYN.SIM.PREFIX, marker.prefix = MARKER.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
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
marker.prefix	(character) prefix for labeling the columns encoding the biomarkers for each group

Value

an ExpressionSet object containing the constructed training sets in the attributes of fData

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