为什么Biomart会给ensembl网站提供不同数量的旁白?
这是我用来提取AA792892基因的同源代码:为什么Biomart会给ensembl网站提供不同数量的旁白?,r,bioinformatics,bioconductor,biomart,R,Bioinformatics,Bioconductor,Biomart,这是我用来提取AA792892基因的同源代码: source("https://bioconductor.org/biocLite.R") biocLite("biomaRt") library(biomaRt) ensembl_mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") AA792892_paralogues <- getBM(attributes
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library(biomaRt)
ensembl_mouse <- useMart("ensembl",
dataset = "mmusculus_gene_ensembl")
AA792892_paralogues <- getBM(attributes = c("external_gene_name",
"mmusculus_paralog_associated_gene_name"),
filters = "external_gene_name",
values = "AA792892" , mart = ensembl_mouse)
View(AA792892_paralogues)
也许软件包和网站使用不同的版本?你能给出其他基因的例子吗?尝试更新biomart,你使用的是旧版本
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.7.4 biomaRt_2.34.2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.15 AnnotationDbi_1.40.0 bindr_0.1
magrittr_1.5 BiocGenerics_0.24.0 progress_1.1.2
IRanges_2.12.0
[8] bit_1.1-12 R6_2.2.2 rlang_0.1.6
httr_1.3.1 stringr_1.2.0 blob_1.1.0 tools_3.4.3
[15] parallel_3.4.3 Biobase_2.38.0 DBI_0.7
yaml_2.1.16 bit64_0.9-7 digest_0.6.15
assertthat_0.2.0
[22] tibble_1.4.2 bindrcpp_0.2 S4Vectors_0.16.0
bitops_1.0-6 curl_3.1 RCurl_1.95-4.10 glue_1.2.0
[29] memoise_1.1.0 RSQLite_2.0 stringi_1.1.6
compiler_3.4.3 pillar_1.1.0 prettyunits_1.0.2 stats4_3.4.3
[36] XML_3.98-1.9 pkgconfig_2.0.1