TROM-package: Transcriptome Overlap Measure
In TROM: Transcriptome Overlap Measure

Description Details Author(s) References Examples

`select.associated.genes`	Select the associated genes of different biological samples
`select.associated.orthologs`	Select the associated genes of different biological samples among
	the genes with orthologs in the other species
`choose.z`	Choose the suggested threshold for Z-scores
`ws.trom`	Within-species transcriptome mapping
`ws.trom.orthologs`	Within-species transcriptome mapping using only ortholog genes
`bs.trom`	Between-species transcriptome mapping
`heatmap.3`	Plot the resulting within- or between-species TROM scores in a heatmap
`find.top.GO.terms`	Find top enriched GO terms
`find.top.GO.slim.terms`	Find top enriched GO slim terms

Package:	TROM
Type:	Package
Version:	1.2
Date:	2016-08-29
License:	GPL-2

Jingyi Jessica Li, Wei Vivian Li

Maintainer: Jingyi Jessica Li jli@stat.ucla.edu

Li WV, Chen Y and Li JJ (2016). TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples. Statistics in Biosciences. DOI: 10.1007/s12561-016-9163-y

Li JJ, Huang H, Bickel PJ, & Brenner SE (2014). Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research, 24(7), 1086-1101.

## using TROM to map developmental stages of D. melanogaster and C. elegans

## The .rda files used in this example can be downloaded and unzipped from
## http://www.stat.ucla.edu/~jingyi.li/packages/TROM/TROM_Rdata.zip.
## Not run: 
load("dm_gene_expr.rda")
load("ce_gene_expr.rda")
load("dm_ce_orthologs.rda")
dm_ce_trom <- bs.trom(sp1_gene_expr = dm_gene_expr,
                      sp2_gene_expr = ce_gene_expr,
                      sp1_sp2_orthologs = dm_ce_orthologs, z_thre=1.5,
                      provide=FALSE)
heatmap.3(   dm_ce_trom,
             max_score = 6,
             Rowv = NULL,
             Colv = NULL,
             dendrogram = c("none"),
             distfun = dist,
             hclustfun = hclust,
             xlab = "worm stages",
             ylab = "fly stages",
             main = "D. melanogaster vs. C. elegans Stage Mapping",
             key = TRUE,
             keysize = 1,
             trace = "none",
             density.info = c("none"),
             col = terrain.colors(120),
  )
  
## End(Not run)