TermAlias: TermAlias
In GEOsearch: GEOsearch
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Search Alias of a Term
Usage
1
Arguments
searchterm
A character value specifying the term being searched. Words should be separated by space.
allspecies
A character vector specifying the species in which the alias of gene names will be searched for. Available species: Anopheles,Arabidopsis,Bovine,Worm,Canine,Fly,Zebrafish,E coli strain K12,E coli strain Sakai,Chicken,Human,Mouse,Rhesus,Malaria,Chimp,Rat,Yeast,Pig,Xenopus
mincount
An integer value specifying the minimum number of appearance in the GEO database for the alias to be retained. If an alias has too few appearance it may not be of great interest.
Details
This function first picks gene names from the searh term. It then searches alias for all the gene names contained in the search term. It next queries GEO and retain alias that appear frequently enough in GEO database. Finally it returns a combinatory results of retained alias.
Value
A character vector of combinatory results of alias.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
Examples
1
TermAlias("Oct4 RNA-seq")
GEOsearch documentation built on Nov. 17, 2017, 8:37 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
Search Alias of a Term
Usage
1 |
Arguments
searchterm |
A character value specifying the term being searched. Words should be separated by space. |
allspecies |
A character vector specifying the species in which the alias of gene names will be searched for. Available species: Anopheles,Arabidopsis,Bovine,Worm,Canine,Fly,Zebrafish,E coli strain K12,E coli strain Sakai,Chicken,Human,Mouse,Rhesus,Malaria,Chimp,Rat,Yeast,Pig,Xenopus |
mincount |
An integer value specifying the minimum number of appearance in the GEO database for the alias to be retained. If an alias has too few appearance it may not be of great interest. |
Details
This function first picks gene names from the searh term. It then searches alias for all the gene names contained in the search term. It next queries GEO and retain alias that appear frequently enough in GEO database. Finally it returns a combinatory results of retained alias.
Value
A character vector of combinatory results of alias.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
Examples
1 | TermAlias("Oct4 RNA-seq")
|
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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