TROM (version 1.1)

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:

1.1

Date:

2015-06-26

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.
## 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)