bioconductor and R, error in the use of getBM() function when trying to retrieving the sequence of genes

Question

I'm trying to use the getBM() function of bioconductor to retrieve the sequences of some gene. Here's my script:

setwd(".")
options(stringsAsFactors = FALSE)
cat("\014")


if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
listOfBiocPackages <- c("annotate", "GEOquery", "biomaRt")

bioCpackagesNotInstalled <- which( !listOfBiocPackages %in% rownames(installed.packages()) )
cat("package missing listOfBiocPackages[", bioCpackagesNotInstalled, "]: ", listOfBiocPackages[bioCpackagesNotInstalled], "\n", sep="")

# check there's still something left to install
if( length(bioCpackagesNotInstalled) ) {
    BiocManager::install(listOfBiocPackages[bioCpackagesNotInstalled])
}

library("easypackages")
libraries(listOfBiocPackages)  

mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useDataset("hsapiens_gene_ensembl", mart)

thisAnnotLookup <- getBM(mart=mart, attributes=c("affy_hg_u133a", "ensembl_gene_id", "gene_biotype", "external_gene_name", "gene_flank"), filter=c("affy_hg_u133a", "upstream_flank"), values=list(affyid=c("203423_at",   "204088_at",   "204511_at",   "204911_s_at", "205234_at")), uniqueRows=TRUE, checkFilters=FALSE)

print(thisAnnotLookup)

This script gives the me following error:

  'names' attribute [2] must be the same length as the vector [1]

which I cannot understand.

Can anyone help me solve this issue? Thanks!

score 0 · Answer 1 · answered Jun 04 '20 at 22:10

You need to provide a list of 2 elements if you have two filters. However the larger problem is that upstream_flank is may not be available depending on your connection, see this problem cropping up for many users. For me, I last used the asia mirror and it worked:

library(biomaRt)

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "asia")

Then:

S = getSequence(id=c("203423_at","204088_at","204511_at","204911_s_at","205234_at"),
type="affy_hg_u133a",seqType="gene_flank",upstream = 20,mart = mart)

thisAnnotLookup <- getBM(mart=mart, 
attributes=c("affy_hg_u133a", "ensembl_gene_id", "gene_biotype", "external_gene_name"), 
filter="affy_hg_u133a", 
values=c("203423_at","204088_at","204511_at","204911_s_at","205234_at"), 
uniqueRows=TRUE, checkFilters=FALSE)

merge(thisAnnotLookup,S)
  affy_hg_u133a ensembl_gene_id   gene_biotype external_gene_name
1     203423_at ENSG00000114115 protein_coding               RBP1
2     204088_at ENSG00000135124 protein_coding              P2RX4
3     204511_at ENSG00000006607 protein_coding              FARP2
4   204911_s_at ENSG00000110171 protein_coding              TRIM3
5     205234_at ENSG00000168679 protein_coding            SLC16A4
            gene_flank
1 CTCCTCTTCCTTTGTAGGGG
2 GATTCCTCTCACCTCGGCCT
3 CGCGGGGGCTGCCGGCGGGC
4 CACCTTTCTACCCCTTAACT
5 GCCTGAGATGACATCAAATC

Seems super finicky to me. I think you are better off using getting the sequence directly off the genome.

bioconductor and R, error in the use of getBM() function when trying to retrieving the sequence of genes

1 Answers1