read.prodigal: Read a Prodigal gene finding output file

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/read.prodigal.R

Description

Read a gff formatted Prodigal gene output file from NCBI (version 2.5)

Usage

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read.prodigal(file, allScores = FALSE)

Arguments

file

Prodigal gff output file

allScores

include all scores

Details

Prodigal output files are available from the NCBI genomes ftp directory, ftp://ftp.ncbi.nih.gov/genomes.

Value

GRanges with 7 elementMetadata columns: id, partial flag for genes continuing off the edge of a contig, start codon, RBS motif, RBS spacer, coding potential/score and start score.

If allScores is TRUE, then four additional score columns are included: total score (sum of coding and start score) and RBS motif score, upstream region score, and codon type score (which usually sum to start score). See the README file in the Prodigal distribution for complete details.

Author(s)

Chris Stubben

References

Prodigal is a microbial gene finding program developed at University of Tennessee and Oak Ridge National Laboratory. See http://prodigal.ornl.gov for details

See Also

read.ncbi.ftp

Examples

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 file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003143.Prodigal-2.50" 
 x <-read.prodigal(file)
 x
 metadata(x)
 table2(values(x)$start_type)
 table2(values(x)$rbs_motif)
 hist(values(x)$sscore, br=40, col="blue", main="", xlab="Start score")

cstubben/genomes2 documentation built on May 12, 2017, 1:19 p.m.