Description Usage Arguments Value References Examples
This method mimics the advanced_search functionality of Colombos. It takes a series of parameters, representing the different settings available on Colombos advanced search and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
1 2 | advanced_search(organism = NULL, g_ids = NULL, geneNames = FALSE, c_ids,
by = "genes", g_search_type, ann_type, c_search_type)
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organism |
A character containing the organism id: use |
g_ids |
A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type. |
geneNames |
boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes. |
c_ids |
A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type. |
by |
A string eithes genes, contrasts, both allowing the selection by genes entities, contrast entities or both. |
g_search_type |
A string either genes, go or annotation. |
ann_type |
A string containing the selected gene_annotation_type: use |
c_search_type |
A string either contrast_names. experiment, go, condition use |
A data.frame containing locustag (gene_names), contrasts and M-values for the current organism and genes.
http://colombos.net
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 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | ## Not run:
library("Rcolombos")
# modules by gene entities
g.gn <- advanced_search(organism="bsubt",
g_ids=c("cgeB","yfnG"),
by="genes", g_search_type="genes")
g.go <- advanced_search(organism="bsubt",
g_ids="response to antibiotic, transcription",
by="genes", g_search_type="go")
g.anno <- advanced_search(organism="bsubt",
g_ids="biotin-carboxyl carrier protein assembly",
by="genes", g_search_type="annotation", ann_type="Pathway")
# modules by contrast entities
c.cn <- advanced_search(organism="bsubt",
c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
by="contrasts", c_search_type="contrast_names")
c.go <- advanced_search(organism="bsubt",
c_ids="response to antibiotic, transcription",
by="contrasts", c_search_type="go")
c.exp <- advanced_search(organism="bsubt",
c_ids="GSE22296", by="contrasts", c_search_type="experiment")
c.cond <- advanced_search(organism="bsubt",
c_ids=c("DAPTOMYCIN","H2O2","HPUra","IPTG","MMC","MNCL2","MOENOMYCIN","RAMOPLANIN"),
by="contrasts", c_search_type="condition")
# modules by both gene and contrast entities
b.go.cn <- advanced_search(organism="bsubt",
g_ids="response to antibiotic, transcription", geneNames=F,
c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
g_search_type="go", c_search_type="contrast_names", by="both")
b.gn.ge <- advanced_search(organism="bsubt", g_ids=c("BSU00020","BSU00100"),
geneNames=F, c_ids="GSE22296", g_search_type="genes",
c_search_type="experiment", by="both")
b.go.ge <- advanced_search(organism="bsubt", g_ids="response to antibiotic, transcription",
geneNames=F, c_ids="GSE22296", g_search_type="go",
c_search_type="experiment", by="both")
b.gn.cn <- advanced_search(organism="bsubt",
g_ids=c("dnaA","dnaN","yaaA","recF","yaaB","gyrB"), geneNames=FALSE,
c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2",
"GSM27219.ch2-vs-GSM27219.ch1","GSM27278.ch2-vs-GSM27278.ch1",
"GSM27279.ch1-vs-GSM27279.ch2"),
g_search_type="genes", c_search_type="contrast_names", by="both")
heatmap(as.matrix(b.gn.cn), col=terrain.colors(15))
## End(Not run)
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