This function tests the consistency and order of a GFF file.
check_gff(inFile, fileType = c("AUTO", "GFF3", "GTF"))A data frame of detected issues, including a short code name, a description and estimated severity each. In no issues are detected the function will return an empty data frame.
Path to the input GFF file
Version of the input file (GTF/GFF3). Default AUTO: determined from the file name.
The following list indicates the code and description of the issues detected in GFF3 files
Input file contains lines with more than 9 fields
Input file contains lines with less than 9 fields
Input file contains too many (more than 100) different feature types
ID attribute not found in any feature
There are duplicated IDs
The same ID has been found in more than one chromosome
Parent attribute not found in any feature
There are missing Parent IDs
There are features whose Parent is located in a different chromosome
Feature ids referenced in Parent attribute before being defined as ID
Features are not grouped by chromosome
Features are not sorted by start coordinate
File cannot be recognized as valid GFF3. Parsing warnings.
File cannot be recognized as valid GFF3. Parsing errors.
The following list indicates the code and description of the issues detected in GTF files
Input file contains lines with more than 9 fields
Input file contains lines with less than 9 fields
Input file contains too many (more than 100) different feature types
gene_id attribute not found in any feature
There are features without gene_id attribute
Gene features are not included in this GTF file
There are duplicated gene_ids
The same gene_id has been found in more than one chromosome
transcript_id attribute not found in any feature There are no elements with transcript_id attribute
There are features without transcript_id attribute
Transcript features are not included in this GTF file
There are duplicated transcript_ids
The same transcript_id has been found in more than one chromosome
Same id has been defined as gene_id and transcript_id
Features are not grouped by chromosome
Features are not sorted by start coordinate
File cannot be recognized as valid GTF. Parsing warnings.
File cannot be recognized as valid GTF. Parsing errors.
test_gff3<-system.file("extdata", "eden.gff3", package="Rgff")
check_gff(test_gff3)
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