Filter genes of interest from GTF file on R

Question

[Bioinf_Questions]

Hello everyone. I'm trying to filter the lines from a GTF file of online the 100 genes I'm interested in using R. The GTF file is already in a dataframe format with one column with the gene_id of each line and the file with the genes of interest also already has only one column with the gene_id of said genes. I've tried to use filter (package: dplyr), but I get the mesage:

> gtf_filtered <- filter(gtf2, gene == top3)
Error in `filter()`:
! Problem while computing `..1 = gene == top3`.
x Input `..1` must be of size 1326608 or 1, not size 100.
Run `rlang::last_error()` to see where the error occurred.

Is there a way to solve this or another package/function I can use to filter the file? Using one gene_id per time doesn't cause any problem (ex:

> gtf_filter_10 <- filter(gtf2, gene == 'gene_id PRX4')   )

Thanks in advance

[cpad0112]

Thank you for describing the data frame in detail. Please post some data and expected output or dput in R.

[Bioinf_Questions]

The data is just a normal gtf file with 9 columns (see http://www.ensembl.org/info/website/upload/gff.html for gtf file details). The list with the genes of interest has just one column with 100 lines with the gene_ids (like 'gene_id PRX4'). The expected output is the same as the original gtf, but with only the wanted genes.

[cpad0112]

Thank you for your data explanation again.

Answer 1

[Chirag Parsania]

gff_file <- "path/to/gff/file"

gff_annot <- rtracklayer::import(gff_file) %>%
    as.data.frame() %>%
    tibble::as_tibble() 

load gene file

gene_file <- "path/to/gene/file"
genes_to_filter <- readr::read_delim(gene_file , delim = "\t") %>% dplyr::pull(1)

filter gff for desired genes

gff_filtered <- gff_annot %>%
    dplyr::filter(gene_id %in% genes_to_filter)  # gene_id is the column name present in the dataframe gff_annot. You can change this as per the column name in your gff file.