cast the gene prediction result as GFF3 table format

as.gff3 {bifrost}

R Documentation

cast the gene prediction result as GFF3 table format

Description

Usage

as.gff3(x);

Arguments

the gene prediction result, which can be the output of "prodigal" function, or a pipeline that produces PredictionResult objects. The pipeline can be created by using the "pipeline" function in R#, and the final output of the pipeline should be PredictionResult objects. For example, if you have a pipeline that produces PredictionResult objects, you can pass it directly to this function to get the GFF3 table format output.

env

the R# runtime environment object. [as Environment]

Authors

seqtoolkit

Value

a GFFTable object that contains all of the predicted genes as the CDS feature, the score of each feature is the total score of the corresponding predicted gene, and the score details are stored in the attributes of the feature, example as start_codon, rbs_motif, cscore, sscore, rscore, tscore, uscore and partial.

this function returns a R# error message object if the input data can not be cast to a collection of the PredictionResult object.

clr value class

GFFTable

[Package bifrost version 1.0.0.0 Index]