TROM (version 1.0)

TROM-package: Transcriptome Overlap Measure

Description

ll{ 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 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 }

Details

ll{ Package: TROM Type: Package Version: 1.0 Date: 2015-04-07 License: GPL-2 }

References

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

## 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.
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, 
                      FPKM_thre=1, 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),
  )