tr2g_GRanges {BUSpaRse} | R Documentation |
Internal use, for GRanges from GTF files
tr2g_GRanges( gr, Genome = NULL, get_transcriptome = TRUE, out_path = ".", write_tr2g = TRUE, transcript_id = "transcript_id", gene_id = "gene_id", gene_name = "gene_name", transcript_version = "transcript_version", gene_version = "gene_version", version_sep = ".", transcript_biotype_col = "transcript_biotype", gene_biotype_col = "gene_biotype", transcript_biotype_use = "all", gene_biotype_use = "all", chrs_only = TRUE, compress_fa = FALSE, save_filtered_gtf = TRUE, overwrite = FALSE )
gr |
A |
Genome |
Either a |
get_transcriptome |
Logical, whether to extract transcriptome from
genome with the GTF file. If filtering biotypes or chromosomes, the filtered
|
out_path |
Directory to save the outputs written to disk. If this directory does not exist, then it will be created. Defaults to the current working directory. |
write_tr2g |
Logical, whether to write tr2g to disk. If |
transcript_id |
Character vector of length 1. Tag in |
gene_id |
Character vector of length 1. Tag in |
gene_name |
Character vector of length 1. Tag in |
transcript_version |
Character vector of length 1. Tag in |
gene_version |
Character vector of length 1. Tag in |
version_sep |
Character to separate bewteen the main ID and the version number. Defaults to ".", as in Ensembl. |
transcript_biotype_col |
Character vector of length 1. Tag in
|
gene_biotype_col |
Character vector of length 1. Tag in |
transcript_biotype_use |
Character, can be "all" or
a vector of transcript biotypes to be used. Transcript biotypes aren't
entirely the same as gene biotypes. For instance, in Ensembl annotation,
|
gene_biotype_use |
Character, can be "all", "cellranger", or
a vector of gene biotypes to be used. If "cellranger", then the biotypes
used by Cell Ranger's reference are used. See |
chrs_only |
Logical, whether to include chromosomes only, for GTF and
GFF files can contain annotations for scaffolds, which are not incorporated
into chromosomes. This will also exclude haplotypes. Defaults to |
compress_fa |
Logical, whether to compress the output fasta file. If
|
save_filtered_gtf |
Logical. If filtering type, biotypes, and/or
chromosomes, whether to save the filtered |
overwrite |
Logical, whether to overwrite if files with names of outputs written to disk already exist. |
A data frame at least 2 columns: gene
for gene ID,
transcript
for transcript ID, and optionally, gene_name
for
gene names.