| Title: | An R Package for Exploring Molecular Signatures Database |
|---|---|
| Description: | The Molecular Signatures Database ('MSigDB') is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis <doi:10.1016/j.cels.2015.12.004>. The 'msig' package provides you with powerful, easy-to-use and flexible query functions for the 'MsigDB' database. There are 2 query modes in the 'msig' package: online query and local query. Both queries contain 2 steps: gene set name and gene. The online search is divided into 2 modes: registered search and non-registered browse. For registered search, email that you registered should be provided. Local queries can be made from local database, which can be updated by msig_update() function. |
| Authors: | Jing Zhang [aut, cre], Zhi Jin [aut] |
| Maintainer: | Jing Zhang <[email protected]> |
| License: | GPL-2 |
| Version: | 1.0 |
| Built: | 2024-12-21 06:50:26 UTC |
| Source: | CRAN |
Retrieve Gene set Names from MSigDB database Retrieve gene set names from MSigDB database by the gene set name and collection. the search filed is gene name.
browse_msig(geneSetName = "", collection = "")browse_msig(geneSetName = "", collection = "")
geneSetName |
one keyword for gene set name, default is empty |
collection |
one collection, default is empty |
gene set names
# missing genSetName and collection to get all gene set names x <- browse_msig() # search for gene names include immune x <- browse_msig('immune') x |> msig_view('cells','response','to','m') # search for gene names include immune in c8 browse_msig('immune','c8') # gene names in c8 browse_msig('immune','c8')# missing genSetName and collection to get all gene set names x <- browse_msig() # search for gene names include immune x <- browse_msig('immune') x |> msig_view('cells','response','to','m') # search for gene names include immune in c8 browse_msig('immune','c8') # gene names in c8 browse_msig('immune','c8')
Show collection of MSigDB database
browse_show_collection()browse_show_collection()
show all collection in MSigDB in web page http://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp. For chromosome, we should treat as collection together.
browse_show_collection()browse_show_collection()
Query gene set names from local data
local_msig( geneset = NULL, description = NULL, collection = NULL, sub_collection = NULL, organism = NULL, contributor = NULL, contributor_org = NULL, author = NULL, chip = NULL, gene = NULL, geneset_fuzzy = NULL, collection_fuzzy = NULL, sub_collection_fuzzy = NULL, organism_fuzzy = NULL, contributor_fuzzy = NULL, contributor_org_fuzzy = NULL, author_fuzzy = NULL, chip_fuzzy = NULL, gene_fuzzy = NULL )local_msig( geneset = NULL, description = NULL, collection = NULL, sub_collection = NULL, organism = NULL, contributor = NULL, contributor_org = NULL, author = NULL, chip = NULL, gene = NULL, geneset_fuzzy = NULL, collection_fuzzy = NULL, sub_collection_fuzzy = NULL, organism_fuzzy = NULL, contributor_fuzzy = NULL, contributor_org_fuzzy = NULL, author_fuzzy = NULL, chip_fuzzy = NULL, gene_fuzzy = NULL )
geneset |
one sql format character for exact match |
description |
one sql format character for exact match |
collection |
one sql format character for exact match |
sub_collection |
one sql format character for exact match |
organism |
one sql format character for exact match |
contributor |
one sql format character for exact match |
contributor_org |
one sql format character for exact match |
author |
one sql format character for exact match |
chip |
one sql format character for exact match |
gene |
one sql format character for exact match |
geneset_fuzzy |
fuzzy match |
collection_fuzzy |
fuzzy match |
sub_collection_fuzzy |
fuzzy match |
organism_fuzzy |
fuzzy match |
contributor_fuzzy |
fuzzy match |
contributor_org_fuzzy |
fuzzy match |
author_fuzzy |
fuzzy match |
chip_fuzzy |
fuzzy match |
gene_fuzzy |
fuzzy match |
one dataframe with attribute of msig_local.
x <- local_msig('IMMUNE_RESPONSE') x <- local_msig('IMMUNE_RESPONSE|IMMUNE_SYSTEM_PROCESS')x <- local_msig('IMMUNE_RESPONSE') x <- local_msig('IMMUNE_RESPONSE|IMMUNE_SYSTEM_PROCESS')
Local database version
local_version()local_version()
version of local database
local_version()local_version()
Retrieve detail information of gene set
msig_detail(...)msig_detail(...)
... |
one or more gene set names, which can be little or capital. |
Print detail information about the geneset, number of genes and return all gene names.
d <- msig_detail('izadpanah_stem_cell_adipose_vs_bone_dn', 'AAACCAC_MIR140')d <- msig_detail('izadpanah_stem_cell_adipose_vs_bone_dn', 'AAACCAC_MIR140')
Download MsigDB database
msig_download(version)msig_download(version)
version |
version |
dowanload the data to local PC
Filt data by key words Case insensitive
msig_filt(x, ...)msig_filt(x, ...)
x |
data from msig package |
... |
one or more key words |
filted results with high light information.
browse_msig('immune') |> msig_filt('response')browse_msig('immune') |> msig_filt('response')
Retrieve gene by Gene set Name
msig_gene(..., list = TRUE, info = TRUE) ## S3 method for class 'character' msig_gene(..., list = TRUE, info = TRUE) ## S3 method for class 'data.frame' msig_gene(..., list = TRUE, info = TRUE)msig_gene(..., list = TRUE, info = TRUE) ## S3 method for class 'character' msig_gene(..., list = TRUE, info = TRUE) ## S3 method for class 'data.frame' msig_gene(..., list = TRUE, info = TRUE)
... |
one or more geneset names, which can be little or capital. |
list |
logical, default is FALSE, whether to show result by list. |
info |
logical, whether to show information about gene set. |
Print detail information about the geneset, number of genes and return all gene names.
genes <- msig_gene('izadpanah_stem_cell_adipose_vs_bone_dn', 'REACTOME_DEGRADATION_OF_AXIN') genes |> msig_view()genes <- msig_gene('izadpanah_stem_cell_adipose_vs_bone_dn', 'REACTOME_DEGRADATION_OF_AXIN') genes |> msig_view()
Retrieve gene by Gene Symbol from MsigDB
msig_geneSymbol(..., local = FALSE) ## S3 method for class 'list' msig_geneSymbol(..., local = FALSE) ## S3 method for class 'data.frame' msig_geneSymbol(..., local = FALSE) ## S3 method for class 'character' msig_geneSymbol(..., local = FALSE)msig_geneSymbol(..., local = FALSE) ## S3 method for class 'list' msig_geneSymbol(..., local = FALSE) ## S3 method for class 'data.frame' msig_geneSymbol(..., local = FALSE) ## S3 method for class 'character' msig_geneSymbol(..., local = FALSE)
... |
one or more geneset names, which can be little or capital. |
local |
logical, default is FALSE, whether to extract gene symbol from local database |
gene symbol
genes <- msig_geneSymbol('izadpanah_stem_cell_adipose_vs_bone_dn') genes <- msig_geneSymbol('izadpanah_stem_cell_adipose_vs_bone_dn', 'REACTOME_DEGRADATION_OF_AXIN')genes <- msig_geneSymbol('izadpanah_stem_cell_adipose_vs_bone_dn') genes <- msig_geneSymbol('izadpanah_stem_cell_adipose_vs_bone_dn', 'REACTOME_DEGRADATION_OF_AXIN')
Update local MsigDB database
msig_update(xml = NULL, version = NULL)msig_update(xml = NULL, version = NULL)
xml |
msigdb xml file |
version |
version, if missing, the latest version will be used |
update local MsigDB database
version information of MSigDB database
msig_version()msig_version()
version dataframe
View data in viewer panel
msig_view(x, ...)msig_view(x, ...)
x |
dataframe |
... |
one or more hightliht words |
open data in view panel in rstudio
#' browse_msig('immune') |> msig_view('response')#' browse_msig('immune') |> msig_view('response')
Create NewMsigDB object for new versions of MsigDB database
NewMsigDB(xml)NewMsigDB(xml)
xml |
path of xml msigdb file path |
dataframe which can be used inner package
read MSigDB xml data
read_msigdb_xml(xml)read_msigdb_xml(xml)
xml |
xml data path |
one dataframe contains gene infomation
Query MSigDB database by cookie
search_msig(keywords, collection = "", organism = "", contributor = "", email)search_msig(keywords, collection = "", organism = "", contributor = "", email)
keywords |
one keywords see Detail field |
collection |
one or more collections |
organism |
one or more organisms |
contributor |
one or more contributors |
email |
email that registered for MSigDB database. |
dataframe contains name, description and so on.
email <- 'your email' x <- search_msig('immune & response') x |> msig_filt('system') |> msig_view('C2')email <- 'your email' x <- search_msig('immune & response') x |> msig_filt('system') |> msig_view('C2')
Show collctions for msigdb_search()
search_show_collection(email)search_show_collection(email)
email |
email that registered for MSigDB database. |
collections from MsigDB website.
search_show_collection("your email") # or email <- 'your email' search_show_collection()search_show_collection("your email") # or email <- 'your email' search_show_collection()
Show contributor for msigdb_search()
search_show_contributor(email)search_show_contributor(email)
email |
email that registered for MSigDB database. |
contributors from MsigDB website.
search_show_contributor("your email") # or email <- 'your email' search_show_contributor()search_show_contributor("your email") # or email <- 'your email' search_show_contributor()
Show organism for msigdb_search()
search_show_organism(email)search_show_organism(email)
email |
email that registered for MSigDB database. |
organisms from MsigDB website.
search_show_organism("your email") # or email <- 'your email' search_show_organism()search_show_organism("your email") # or email <- 'your email' search_show_organism()
Show collections of local MsigDB database
show_local_collection()show_local_collection()
A dataframe contains 2 columns. The first column is the name of the collection. The second column is the number of frequencies it has.
show_local_collection()show_local_collection()
Show contributors of local MsigDB database
show_local_contributor()show_local_contributor()
A dataframe contains 2 columns. The first column is the name of the contributor. The second column is the number of frequencies it has.
show_local_contributor()show_local_contributor()
Show contributor_orgs of local MsigDB database
show_local_contributor_org()show_local_contributor_org()
A dataframe contains 2 columns. The first column is the name of the contributor_org. The second column is the number of frequencies it has.
show_local_contributor_org()show_local_contributor_org()
Show local data used in this package
show_local_data()show_local_data()
data used inner this package
show_local_data()show_local_data()
Show sub_collections of local MsigDB database
Show sub_collections of local MsigDB database
show_local_sub_collection() show_local_sub_collection()show_local_sub_collection() show_local_sub_collection()
A dataframe contains 2 columns. The first column is the name of the sub_collection. The second column is the number of frequencies it has.
A dataframe contains 2 columns. The first column is the name of the sub_collection. The second column is the number of frequencies it has.
show_local_sub_collection() show_local_sub_collection()show_local_sub_collection() show_local_sub_collection()
Query similarity gene sets
similarity_geneset(geneSetName)similarity_geneset(geneSetName)
geneSetName |
one gene set name |
similarity gene sets
x <- similarity_geneset('REACTOME_DEGRADATION_OF_AXIN') x |> msig_view()x <- similarity_geneset('REACTOME_DEGRADATION_OF_AXIN') x |> msig_view()