This is the code I am using to extract paralogues for the AA792892 gene:
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)
The results show that there are 99 paralogues in total, but when looking at the Ensembl website, it says that there are 100 for this gene. This is happening for quite a few genes and I cant work out why.
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
