TROM-package: Transcriptome Overlap Measure

Description Details Author(s) References Examples

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
find.top.GO.slim.terms Find top enriched GO slim terms

Details

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

Author(s)

Jingyi Jessica Li, Wei Vivian Li

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

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

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## 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)

TROM documentation built on May 1, 2019, 8:07 p.m.