c3-package: C3: Cross-species compendium-based cell-type identification

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

Description

C3 is an R package for cross-species compendium-based cell-type identification. This package contains the neccessary R code to run C3 as described in "C3: An R package for compendium-based cross-species cell-type identification". C3 is implemented within a helpful framework to identify an unknown cell-type from a transcriptomic profile.

Author(s)

Md Humayun Kabir <[e-mail]>

Examples

## Do a sample analysis using human compendium data and mouse lens query data.

## Make human gene expression compendium from ENCODE data
human.compendium<-make_gene_expression_compendium(gene.expression.data = human.encode.data, species = "hsapiens", experiment.descriptor = human.encode.data.descriptor, expression.data.format = "list")
## Add Hawse et al. human lens transcriptome to the compendium
Hawse.data.descriptor<-c("Hawse_LEC","Hawse_LEC","Hawse_LEC","Hawse_LFC","Hawse_LFC","Hawse_LFC")
Hawse.human.compendium<-add_sample_into_compendium(compendium.data = human.compendium, sample.data = hawse.human.lens.data, species = "hsapiens", data.format = "matrix", geneID = "external_gene_name", experiment.descriptor = Hawse.data.descriptor)
## Convert to a tissue / cell type specific marker gene compendium
human.marker.gene.compendium<-make_marker_gene_compendium(compendium.data = Hawse.human.compendium, specific.cutoff = 0.05, top.expressed.genes = 500)
## Pre-process the mouse lens transcriptome query data
Hoang.processed.query.data<-preprocess_querydata(cell.tissue.data = hoang.mouse.lens.data, species = "mmusculus", data.format = "matrix", geneID = "external_gene_name")
## C3 testing of mouse lens query vs. human marker gene compendium
Hoang.data.test.result<-c3_test(processed.queryData = Hoang.processed.query.data, marker.gene.compendium = human.marker.gene.compendium)
## Display C3 test result
par(mar=c(10,10,5,5))
c3_display_result(Hoang.data.test.result)

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