| Title: | An R Package for Exploring Molecular Signatures Database |
| Version: | 1.0 |
| 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. |
| License: | GPL-2 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.1 |
| Imports: | do, rvest, xml2, set, plyr, httr, jsonlite, utils, kableExtra, tmcn, crayon, dplyr, stringr, sqldf |
| Depends: | R (≥ 4.1.0) |
| NeedsCompilation: | no |
| Packaged: | 2021-06-27 00:14:35 UTC; asus |
| Author: | Jing Zhang [aut, cre], Zhi Jin [aut] |
| Maintainer: | Jing Zhang <zj391120@163.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-06-29 07:50:02 UTC |
Create NewMsigDB object for new versions of MsigDB database
Description
Create NewMsigDB object for new versions of MsigDB database
Usage
NewMsigDB(xml)
Arguments
xml |
path of xml msigdb file path |
Value
dataframe which can be used inner package
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.
Description
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.
Usage
browse_msig(geneSetName = "", collection = "")
Arguments
geneSetName |
one keyword for gene set name, default is empty |
collection |
one collection, default is empty |
Value
gene set names
Examples
# 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
Description
Show collection of MSigDB database
Usage
browse_show_collection()
Value
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.
Examples
browse_show_collection()
Query gene set names from local data
Description
Query gene set names from local data
Usage
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
)
Arguments
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 |
Value
one dataframe with attribute of msig_local.
Examples
x <- local_msig('IMMUNE_RESPONSE')
x <- local_msig('IMMUNE_RESPONSE|IMMUNE_SYSTEM_PROCESS')
Local database version
Description
Local database version
Usage
local_version()
Value
version of local database
Examples
local_version()
Retrieve detail information of gene set
Description
Retrieve detail information of gene set
Usage
msig_detail(...)
Arguments
... |
one or more gene set names, which can be little or capital. |
Value
Print detail information about the geneset, number of genes and return all gene names.
Examples
d <- msig_detail('izadpanah_stem_cell_adipose_vs_bone_dn',
'AAACCAC_MIR140')
Download MsigDB database
Description
Download MsigDB database
Usage
msig_download(version)
Arguments
version |
version |
Value
dowanload the data to local PC
Filt data by key words Case insensitive
Description
Filt data by key words Case insensitive
Usage
msig_filt(x, ...)
Arguments
x |
data from msig package |
... |
one or more key words |
Value
filted results with high light information.
Examples
browse_msig('immune') |>
msig_filt('response')
Retrieve gene by Gene set Name
Description
Retrieve gene by Gene set Name
Usage
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)
Arguments
... |
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. |
Value
Print detail information about the geneset, number of genes and return all gene names.
Examples
genes <- msig_gene('izadpanah_stem_cell_adipose_vs_bone_dn',
'REACTOME_DEGRADATION_OF_AXIN')
genes |>
msig_view()
Retrieve gene by Gene Symbol from MsigDB
Description
Retrieve gene by Gene Symbol from MsigDB
Usage
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)
Arguments
... |
one or more geneset names, which can be little or capital. |
local |
logical, default is FALSE, whether to extract gene symbol from local database |
Value
gene symbol
Examples
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
Description
Update local MsigDB database
Usage
msig_update(xml = NULL, version = NULL)
Arguments
xml |
msigdb xml file |
version |
version, if missing, the latest version will be used |
Value
update local MsigDB database
version information of MSigDB database
Description
version information of MSigDB database
Usage
msig_version()
Value
version dataframe
View data in viewer panel
Description
View data in viewer panel
Usage
msig_view(x, ...)
Arguments
x |
dataframe |
... |
one or more hightliht words |
Value
open data in view panel in rstudio
Examples
#' browse_msig('immune') |>
msig_view('response')
read MSigDB xml data
Description
read MSigDB xml data
Usage
read_msigdb_xml(xml)
Arguments
xml |
xml data path |
Value
one dataframe contains gene infomation
Query related gene sets
Description
Query related gene sets
Usage
related_geneset(geneSetName)
Arguments
geneSetName |
one gene set name |
Value
related gene sets from gene set detailed information table
Examples
x <- related_geneset('AAANWWTGC_UNKNOWN')
x |>
msig_filt('unknown') |>
msig_view('ttt')
Query MSigDB database by cookie
Description
Query MSigDB database by cookie
Usage
search_msig(keywords, collection = "", organism = "", contributor = "", email)
Arguments
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. |
Value
dataframe contains name, description and so on.
Examples
email <- 'your email'
x <- search_msig('immune & response')
x |>
msig_filt('system') |>
msig_view('C2')
Show collctions for msigdb_search()
Description
Show collctions for msigdb_search()
Usage
search_show_collection(email)
Arguments
email |
email that registered for MSigDB database. |
Value
collections from MsigDB website.
Examples
search_show_collection("your email")
# or
email <- 'your email'
search_show_collection()
Show contributor for msigdb_search()
Description
Show contributor for msigdb_search()
Usage
search_show_contributor(email)
Arguments
email |
email that registered for MSigDB database. |
Value
contributors from MsigDB website.
Examples
search_show_contributor("your email")
# or
email <- 'your email'
search_show_contributor()
Show organism for msigdb_search()
Description
Show organism for msigdb_search()
Usage
search_show_organism(email)
Arguments
email |
email that registered for MSigDB database. |
Value
organisms from MsigDB website.
Examples
search_show_organism("your email")
# or
email <- 'your email'
search_show_organism()
Show collections of local MsigDB database
Description
Show collections of local MsigDB database
Usage
show_local_collection()
Value
A dataframe contains 2 columns. The first column is the name of the collection. The second column is the number of frequencies it has.
Examples
show_local_collection()
Show contributors of local MsigDB database
Description
Show contributors of local MsigDB database
Usage
show_local_contributor()
Value
A dataframe contains 2 columns. The first column is the name of the contributor. The second column is the number of frequencies it has.
Examples
show_local_contributor()
Show contributor_orgs of local MsigDB database
Description
Show contributor_orgs of local MsigDB database
Usage
show_local_contributor_org()
Value
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.
Examples
show_local_contributor_org()
Show local data used in this package
Description
Show local data used in this package
Usage
show_local_data()
Value
data used inner this package
Examples
show_local_data()
Show sub_collections of local MsigDB database
Description
Show sub_collections of local MsigDB database
Show sub_collections of local MsigDB database
Usage
show_local_sub_collection()
show_local_sub_collection()
Value
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.
Examples
show_local_sub_collection()
show_local_sub_collection()
Query similarity gene sets
Description
Query similarity gene sets
Usage
similarity_geneset(geneSetName)
Arguments
geneSetName |
one gene set name |
Value
similarity gene sets
Examples
x <- similarity_geneset('REACTOME_DEGRADATION_OF_AXIN')
x |>
msig_view()