readTrinOutput: Read, process, and trim Trinotate output

In saraihs2/GOsorting: GO sorting and matching of terms found enriched in the honey bee brain during defense

Description

Reads .CSV files only. The function processes differentially expressed RNA data that has been analyzed for Gene Ontology enrichment. Function reads in data, processes out data with unidentified genes, and trims data columns needed for GO matching. Function is compatible with the the .CSV-converted output file format from Trinotate:Transcriptome Functional Annotation and Analysis suite.

Usage

readTrinOutput(path)

Arguments

path	User provided path to .CSV Trinotate-formated file

Value

Returns a data frame with the columns of the following headers : gene_id, transcript_id, gene_ontology_blast, gene_ontology_pfam

Rows without a gene_id are filtered out

Output is the argument for GOtermSep Function

Author(s)

Sarai Stuart

References

https://trinotate.github.io/

See Also

GOtermSep

Examples

#Path to test file
path <- system.file("extdata", 
                       "New_GO_test_file.csv",
                       package = "GOsorting")
                       
test.csv <- read.csv(path)

#Insert "path" argument into function
test <- readTrinOutput(test.csv)

saraihs2/GOsorting documentation built on May 12, 2019, 8:45 a.m.