extract_field_from_gencode: Extract field from gencode GTF file
In jokergoo/cotools: R functions
Description
Usage
Arguments
Details
Value
Examples
Description
Extract field from gencode GTF file
Usage
1
extract_field_from_gencode(file, level = "gene", primary_key = "gene_id", field = "gene_name")
Arguments
file
the input gtf file
level
level of the annotation (e.g. gene, transcript, exon, ...)
primary_key
primary field
field
field to be retrieved
Details
Although gtf file can be imported by makeTranscriptDbFromGFF, some information
in the original gtf file will not be imported. This function aims to extract additionally information
from gtf file.
The function calls external perl script, so you need to have perl installed.
Value
A vector in which 'primary_key' corresponds to the name and 'field' corresponds to the value
Examples
1
2
# There is no example
NULL
jokergoo/cotools documentation built on May 19, 2019, 6:24 p.m.
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Description Usage Arguments Details Value Examples
Description
Extract field from gencode GTF file
Usage
1 | extract_field_from_gencode(file, level = "gene", primary_key = "gene_id", field = "gene_name")
|
Arguments
file |
the input gtf file |
level |
level of the annotation (e.g. gene, transcript, exon, ...) |
primary_key |
primary field |
field |
field to be retrieved |
Details
Although gtf file can be imported by makeTranscriptDbFromGFF, some information
in the original gtf file will not be imported. This function aims to extract additionally information
from gtf file.
The function calls external perl script, so you need to have perl installed.
Value
A vector in which 'primary_key' corresponds to the name and 'field' corresponds to the value
Examples
1 2 | # There is no example
NULL
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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