Option set for cuffgffread
A CuffGFFReadOptions
object contains options for the
cuffgffread
function, which filters and converts GFF and GTF files
[1].
creates
a cuffgffreadOpt
= CuffGFFReadOptionsCuffGFFReadOptions
object with the default property values.
CuffGFFReadOptions
requires the Cufflinks Support Package for the Bioinformatics Toolbox™. If the support package is not installed, then the function provides a download
link. For details, see Bioinformatics Toolbox Software Support Packages.
Note
CuffGFFReadOptions
is supported on the Mac and UNIX® platforms only.
sets the object properties using
one or more name-value pair arguments. Enclose each property name in quotes. For example,
cuffgffreadOpt
= CuffGFFReadOptions(Name,Value)cuffgffreadOpt = CuffGFFReadOptions('DiscardSingleExon',true)
discards transcripts spanning a single exon.
specifies optional parameters using the string or character vector
cuffgffreadOpt
= CuffGFFReadOptions(S
)S
.
getCommand | Translate object properties to original options syntax |
getOptionsTable | Return table with all properties and equivalent options in original syntax |
[1] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.