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#Load library
library(biomaRt)## Warning: package 'biomaRt' was built under R version 3.6.3#List databases, click on myMarts in Environment to view options
myMarts <- listMarts()
#Select database, for assignment CHANGE to Ensembl Variation
ensembl=useMart("ENSEMBL_MART_ENSEMBL")
#List datasets, click on myDatasets in Environment to view options
myDatasets<-listDatasets(ensembl)
#Select dataset, for assignment CHANGE to short Human variants
ensembl=useMart("ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl")
#List filters, click on myFilters in Environment to view options
myFilters <- listFilters(ensembl)
#Make a vector for your filters
filter1 <- c('chromosome_name', 'start', 'end')
#Make a vector for the values that will go into your filter
#Change this for the assignment to be the list of 100
#rsids from last week
values1 <- list(1, 82154, 1191870)
#List attributes, click on myAttributes in Environment to view options
myAttributes <- listAttributes(ensembl)
#Make a variable for your attributes
att1 <- c('ensembl_gene_id','chromosome_name','start_position')
searchResults <-getBM(att1,
filters= filter1,
values= values1, mart=ensembl)## Cache foundsearchResults## ensembl_gene_id chromosome_name start_position
## 1 ENSG00000238009 1 89295
## 2 ENSG00000239945 1 89551
## 3 ENSG00000233750 1 131025
## 4 ENSG00000268903 1 135141
## 5 ENSG00000269981 1 137682
## 6 ENSG00000239906 1 139790
## 7 ENSG00000241860 1 141474
## 8 ENSG00000222623 1 157784
## 9 ENSG00000241599 1 160446
## 10 ENSG00000279928 1 182696
## 11 ENSG00000279457 1 185217
## 12 ENSG00000273874 1 187891
## 13 ENSG00000228463 1 257864
## 14 ENSG00000286448 1 266855
## 15 ENSG00000236679 1 347982
## 16 ENSG00000236601 1 358857
## 17 ENSG00000237094 1 365389
## 18 ENSG00000269732 1 439870
## 19 ENSG00000284733 1 450703
## 20 ENSG00000233653 1 487101
## 21 ENSG00000250575 1 491225
## 22 ENSG00000278757 1 516376
## 23 ENSG00000230021 1 586071
## 24 ENSG00000235146 1 587629
## 25 ENSG00000225972 1 629062
## 26 ENSG00000225630 1 629640
## 27 ENSG00000237973 1 631074
## 28 ENSG00000278791 1 632325
## 29 ENSG00000229344 1 632757
## 30 ENSG00000240409 1 633535
## 31 ENSG00000248527 1 633696
## 32 ENSG00000198744 1 634376
## 33 ENSG00000268663 1 674842
## 34 ENSG00000284662 1 685679
## 35 ENSG00000229376 1 722092
## 36 ENSG00000228327 1 725885
## 37 ENSG00000223181 1 758233
## 38 ENSG00000229905 1 760911
## 39 ENSG00000237491 1 778747
## 40 ENSG00000285268 1 781937
## 41 ENSG00000230092 1 800879
## 42 ENSG00000177757 1 817371
## 43 ENSG00000228794 1 825138
## 44 ENSG00000225880 1 826206
## 45 ENSG00000288531 1 860226
## 46 ENSG00000230368 1 868071
## 47 ENSG00000234711 1 873292
## 48 ENSG00000283040 1 874529
## 49 ENSG00000272438 1 904834
## 50 ENSG00000230699 1 911435
## 51 ENSG00000241180 1 914171
## 52 ENSG00000223764 1 916865
## 53 ENSG00000187634 1 923928
## 54 ENSG00000188976 1 944203
## 55 ENSG00000187961 1 960584
## 56 ENSG00000187583 1 966482
## 57 ENSG00000187642 1 975204
## 58 ENSG00000272512 1 995966
## 59 ENSG00000188290 1 998962
## 60 ENSG00000187608 1 1001138
## 61 ENSG00000231702 1 1008076
## 62 ENSG00000224969 1 1011997
## 63 ENSG00000188157 1 1020120
## 64 ENSG00000242590 1 1055033
## 65 ENSG00000217801 1 1059708
## 66 ENSG00000273443 1 1062208
## 67 ENSG00000237330 1 1070967
## 68 ENSG00000131591 1 1081818
## 69 ENSG00000285812 1 1097585
## 70 ENSG00000223823 1 1137017
## 71 ENSG00000207730 1 1167104
## 72 ENSG00000207607 1 1167863
## 73 ENSG00000198976 1 1169005
## 74 ENSG00000272141 1 1169357
## 75 ENSG00000205231 1 1173056
## 76 ENSG00000162571 1 1173880