Rcolombos (version 2.0.2)

advanced_search: 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.

Description

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.

Usage

advanced_search(organism = NULL, g_ids = NULL, geneNames = FALSE, c_ids, by = "genes", g_search_type, ann_type, c_search_type)

Arguments

organism

A character containing the organism id: use listOrganisms to display the available organisms.

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 listEntities to display the available entities.

c_search_type

A string either contrast_names. experiment, go, condition use listOrganisms to display the available organisms.

Value

A data.frame containing locustag (gene_names), contrasts and M-values for the current organism and genes.

References

http://colombos.net

Examples

## 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)