Based on the human cell cycle genes, the cell cycle genes of the corresponding species were captured by homologous gene conversion.
Usage
CC_GenePrefetch(
species = "Homo_sapiens",
Ensembl_version = 103,
mirror = NULL,
max_tries = 5,
use_cached_gene = TRUE,
verbose = TRUE
)Arguments
- species
Latin names for animals,i.e., "Homo_sapiens", "Mus_musculus"
- Ensembl_version
Ensembl database version. If NULL, use the current release version.
- mirror
Specify an Ensembl mirror to connect to. The valid options here are 'www', 'uswest', 'useast', 'asia'.
- max_tries
The maximum number of attempts to connect with the BioMart service.
- use_cached_gene
Whether to use previously cached cell cycle gene conversion results for the species.
- verbose
Whether to print messages.
Examples
ccgenes <- CC_GenePrefetch("Homo_sapiens")
#> ℹ [2025-07-26 06:24:23] Prefetching cell cycle genes forHomo_sapiens...
#> ✔ [2025-07-26 06:24:23] Cell cycle gene prefetching completed
str(ccgenes)
#> List of 3
#> $ res: NULL
#> $ S : chr [1:43] "MCM5" "PCNA" "TYMS" "FEN1" ...
#> $ G2M: chr [1:54] "HMGB2" "CDK1" "NUSAP1" "UBE2C" ...
ccgenes <- CC_GenePrefetch("Mus_musculus")
#> ℹ [2025-07-26 06:24:23] Prefetching cell cycle genes forMus_musculus...
#> ℹ [2025-07-26 06:24:23] Connect to the Ensembl archives...
#> ℹ [2025-07-26 06:24:23] Using the 103 version of biomart...
#> ℹ [2025-07-26 06:24:23] Connecting to the biomart...
#> ℹ [2025-07-26 06:25:23] Error in `req_perform()`:
#> ℹ [2025-07-26 06:25:23] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:25:23] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:25:23] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:25:23] Operation timed out after 60000 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:25:23]
#> ℹ [2025-07-26 06:25:23] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 06:25:24] Retrying...
#> ℹ [2025-07-26 06:26:24] Error in `req_perform()`:
#> ℹ [2025-07-26 06:26:24] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:26:24] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:26:24] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:26:24] Operation timed out after 60001 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:26:24]
#> ℹ [2025-07-26 06:26:24] Get errors when connecting with ensembl mart...
#> ℹ [2025-07-26 06:26:25] Retrying...
#> ℹ [2025-07-26 06:26:26] Searching the dataset hsapiens ...
#> ℹ [2025-07-26 06:26:26] Connecting to the dataset hsapiens_gene_ensembl ...
#> ℹ [2025-07-26 06:27:27] Error in `req_perform()`:
#> ℹ [2025-07-26 06:27:27] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:27:27] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:27:27] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:27:27] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:27:27]
#> ℹ [2025-07-26 06:27:27] Get errors when connecting with Dataset(hsapiens_gene_ensembl)
#> ℹ [2025-07-26 06:27:28] Retrying...
#> ℹ [2025-07-26 06:28:28] Error in `req_perform()`:
#> ℹ [2025-07-26 06:28:28] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:28:28] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:28:28] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:28:28] Operation timed out after 60000 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:28:28]
#> ℹ [2025-07-26 06:28:28] Get errors when connecting with Dataset(hsapiens_gene_ensembl)
#> ℹ [2025-07-26 06:28:29] Retrying...
#> ℹ [2025-07-26 06:29:29] Error in `req_perform()`:
#> ℹ [2025-07-26 06:29:29] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:29:29] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:29:29] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:29:29] Operation timed out after 60000 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:29:29]
#> ℹ [2025-07-26 06:29:29] Get errors when connecting with Dataset(hsapiens_gene_ensembl)
#> ℹ [2025-07-26 06:29:30] Retrying...
#> ℹ [2025-07-26 06:30:30] Error in `req_perform()`:
#> ℹ [2025-07-26 06:30:30] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:30:30] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:30:30] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:30:30] Operation timed out after 60000 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:30:30]
#> ℹ [2025-07-26 06:30:30] Get errors when connecting with Dataset(hsapiens_gene_ensembl)
#> ℹ [2025-07-26 06:30:31] Retrying...
#> ℹ [2025-07-26 06:31:31] Error in `req_perform()`:
#> ℹ [2025-07-26 06:31:31] ! Failed to perform HTTP request.
#> ℹ [2025-07-26 06:31:31] Caused by error in `curl::curl_fetch_memory()`:
#> ℹ [2025-07-26 06:31:31] ! Timeout was reached [feb2021.archive.ensembl.org]:
#> ℹ [2025-07-26 06:31:31] Operation timed out after 60002 milliseconds with 0 bytes received
#> ℹ [2025-07-26 06:31:31]
#> ℹ [2025-07-26 06:31:31] Get errors when connecting with Dataset(hsapiens_gene_ensembl)
#> Error in log_message(out, message_type = "error"): Error in `req_perform()`: ! Failed to perform HTTP request. Caused by
#> error in `curl::curl_fetch_memory()`: ! Timeout was reached
#> [feb2021.archive.ensembl.org]: Operation timed out after 60002 milliseconds
#> with 0 bytes received
str(ccgenes)
#> List of 3
#> $ res: NULL
#> $ S : chr [1:43] "MCM5" "PCNA" "TYMS" "FEN1" ...
#> $ G2M: chr [1:54] "HMGB2" "CDK1" "NUSAP1" "UBE2C" ...