Description
Usage
Arguments
Value
View source: R/tr2g.R
Internal use, for GRanges from GTF files
| (gr, type_use = "exon", transcript_id = "transcript_id",
gene_id = "gene_id", gene_name = "gene_name",
transcript_version = "transcript_version",
gene_version = "gene_version", version_sep = ".")
|
gr |
A GRanges object. The metadata columns should be
atomic vectors, not lists.
|
type_use |
Character vector, the values taken by the type field
in the GTF file that denote the desired transcripts. This can be "exon",
"transcript", "mRNA", and etc.
|
transcript_id |
Character vector of length 1. Tag in attribute
field corresponding to transcript IDs. This argument must be supplied and
cannot be NA or NULL . Will throw error if tag indicated in this
argument does not exist.
|
gene_id |
Character vector of length 1. Tag in attribute
field corresponding to gene IDs. This argument must be supplied and
cannot be NA or NULL . Note that this is different from gene
symbols, which do not have to be unique. This can be Ensembl or Entrez IDs.
However, if the gene symbols are in fact unique for each gene, you may
supply the tag for human readable gene symbols to this argument. Will throw
error if tag indicated in this argument does not exist.
|
gene_name |
Character vector of length 1. Tag in attribute
field corresponding to gene symbols. This argument can be NA or
NULL if you are fine with non-human readable gene IDs and do not wish
to extract human readable gene symbols.
|
transcript_version |
Character vector of length 1. Tag in attribute
field corresponding to transcript version number. If your GTF file does not
include transcript version numbers, or if you do not wish to include the
version number, then use NULL for this argument. To decide whether to
include transcript version number, check whether version numbers are included
in the transcripts.txt in the kallisto output directory. If that file
includes version numbers, then trannscript version numbers must be included
here as well. If that file does not include version numbers, then transcript
version numbers must not be included here.
|
gene_version |
Character vector of length 1. Tag in attribute
field corresponding to gene version number. If your GTF file does not
include gene version numbers, or if you do not wish to include the
version number, then use NULL for this argument. Unlike transcript
version number, it's up to you whether to include gene version number.
|
version_sep |
Character to separate bewteen the main ID and the version
number. Defaults to ".", as in Ensembl.
|
A data frame at least 2 columns: gene
for gene ID,
transcript
for transcript ID, and optionally, gene_name
for
gene names.
sarangian/RNASeqDEA documentation built on Dec. 8, 2019, 5:24 p.m.