How to import a gtf file in R so that it appears in tabular format as if it were a data frame?
Hi all!
How to import a gtf file in R so that it appears in tabular format as if it were a data frame?
This is the file name:
GCF_023701775.1_HaSCD2_genomic.gtf
This is the file head:
#gtf-version 2.2
#!genome-build HaSCD2
#!genome-build-accession NCBI_Assembly:GCF_023701775.1
#!annotation-source NCBI RefSeq Helicoverpa armigera Annotation Release 101
NC_064776.1 Gnomon gene 4347 6338 . - . gene_id "LOC126054536"; transcript_id ""; db_xref "GeneID:126054536"; description "uncharacterized LOC126054536"; gbkey "Gene"; gene "LOC126054536"; gene_biotype "protein_coding";
2 answers
library(rtracklayer)
GTF <- rtracklayer::import('your.gtf')
GTF <- data.frame(GTF)
although i would opt for a txdb if you are working in R
library(GenomicFeatures)
txdb <- makeTxDbFromGFF('your.gtf')
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benformatics
If you find that the functions from the rtracklayer or GenomicsFeatures libraries don't work for your annotations, you can try my read_gtf() function:
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It's just a tab-separated file. You can use
read.delim(filename, sep="\t", skip=n)where n = header lines. Is that really what you want?Actually tab-separated with nested columns separated by semicolon, so the rtracklayer route should be preferred since it takes care of separating those columns-in-columns.
Thus my question to the OP..."Is that really what you want?" as it wasn't clear to me what they were trying to accomplish with a data frame. But yes, I figured the real solution would involve txdb or rtracklayer, which are both great for this.