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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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)
|
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