TROM (version 1.3)

TROM-package: Transcriptome Overlap Measure

Description

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

Details

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

References

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.

Examples

# NOT RUN {
## 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),
  )
  
# }