change gene id to gene name

Question

[Andy]

Hello everyone,

I noticed that one RDS file I want to use only provide gene id not gene name.

It looks like:

str(data@assays$RNA@counts)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:1421002083] 23 26 39 43 53 55 66 68 86 89 ...
  ..@ p       : int [1:714332] 0 3420 4066 7251 8853 11471 15253 15958 16971 19599 ...
  ..@ Dim     : int [1:2] 33234 714331
  ..@ Dimnames:List of 2
  .. ..$ : chr [1:33234] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
  .. ..$ : chr [1:714331] "r1_hbca_c01_AACCATGGTATGCTTG" "r1_hbca_c01_ACGGAGACAAGCTGTT" "r1_hbca_c01_ACTGATGGTCATCGGC" "r1_hbca_c01_AGGTCATGTGCACCAC" ...
  ..@ x       : num [1:1421002083] 1 1 1 1 2 1 4 1 1 1 ...
  ..@ factors : list()

I tried to use hg19 reference file to change it, however, I failed. The code works fine but the it did not changed the result.

My code is:

>library(GenomicFeatures)

>gtf_file <- "~/humanreference/hg19/genes/genes.gtf"


>txdb <- makeTxDbFromUCSC(gtf_file, organism = "Homo sapiens")

>gene_ids_gtf <- keys(txdb, keytype = "GENEID")

>gene_names_gtf <- keys(txdb, keytype = "GENENAME")

>id_to_name_gtf <- setNames(gene_names_gtf, gene_ids_gtf)

>gene_names_gtf <- id_to_name_gtf[gene_ids]

after I run these codes above, my str(data@assays$RNA@counts) still looks same.

I am not sure how to solve this problem. Hope you can help me out. Andy

[Ming Tommy Tang]

you did not change anything in the counts yet.

you may want to change the original count matrix's rownames and then create a Seurat object with that new matrix