select_query_sample_specific_genes: select_query_sample_specific_genes

In VCCRI/C3: An R package for cross-species compendium-based cell-type identification for transcriptomic profile

Description

This function converts the query data into a list of XGSA data sets containing the marker genes for each sample.

Usage

select_query_sample_specific_genes(processed.queryData, comSpecies, topExpGenes,
  compendiumCommonGenes)

Arguments

processed.queryData	A list containing the average gene expression values for the cell types and/or tissues with ensembl gene IDs and the species name, as returned by 'preprocess_querydata'.
comSpecies	The species of the compendium which the query is being compared to. Default is "hsapiens".
topExpGenes	The number of highest expressed genes from each cell/tissue that will be considered for marker gene status.
compendiumCommonGenes	The list of commonly expressed (non-marker) genes as determined from the compendium, which will be removed from the list of highly expressed sample genes.

Details

This function converts the query data into a list of XGSA data sets containing the marker genes for each sample.

Value

This function returns a list containing XGSA data sets ready to test with the compendium data.

Examples

Used within C3 framework

VCCRI/C3 documentation built on May 14, 2019, 8:41 a.m.