The goal of genesets
is to collect many useful gene sets for cancer
bioinformatics analysis.
You can install the developing version of genesets
from
Github with:
devtools::install_github("Moonerss/genesets")
All the gene sets list can be seen by:
library(genesets)
available_genesets()
[1] "CancerSEA" "Hallmark" "Immport"
To search a special gene sets, you can use search_genesets()
:
search_genesets(keywords = "SEA")
[1] "CancerSEA"
The structure of each gene set like this:
str(CancerSEA)
List of 14
$ angiogenesis :'data.frame': 73 obs. of 2 variables:
..$ ensembl_gene_id: chr [1:73] "ENSG00000139567" "ENSG00000101384" "ENSG00000154188" "ENSG00000091879" ...
..$ symbol : chr [1:73] "ACVRL1" "JAG1" "ANGPT1" "ANGPT2" ...
..- attr(*, "spec")=
.. .. cols(
.. .. EnsembleID = col_character(),
.. .. GeneName = col_character()
.. .. )
$ apoptosis :'data.frame': 66 obs. of 2 variables:
..$ ensembl_gene_id: chr [1:66] "ENSG00000120868" "ENSG00000128272" "ENSG00000149311" "ENSG00000030110" ...
..$ symbol : chr [1:66] "APAF1" "ATF4" "ATM" "BAK1" ...
..- attr(*, "spec")=
.. .. cols(
.. .. EnsembleID = col_character(),
.. .. GeneName = col_character()
.. .. )
Each particular pathway or functional gene set contain two column:
ensembl_gene_id
symbol
CancerSEA$angiogenesis
# A tibble: 73 x 2
ensembl_gene_id symbol
<chr> <chr>
1 ENSG00000139567 ACVRL1
2 ENSG00000101384 JAG1
3 ENSG00000154188 ANGPT1
4 ENSG00000091879 ANGPT2
5 ENSG00000174059 CD34
6 ENSG00000070831 CDC42
7 ENSG00000112062 MAPK14
8 ENSG00000025708 TYMP
9 ENSG00000078401 EDN1
10 ENSG00000125266 EFNB2
# ... with 63 more rows