GsnapOutput-class: Class '"GsnapOutput"'

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

Description

A GsnapOutput object stores locations of data output by the GSNAP alignment algorithm.

Objects from the Class

GsnapOutput objects are created from the gsnap function, though the function GsnapOutput can also be used as a constructor.

Coercion

In the code snippets below, x is a GsnapOutput object.

as(x, BamFile), as(x, BamFileList):

Returns either a BamFile or BamFileList object containing paths to the output of GSNAP.

asBam(x):

converts all gsnap SAM files to BAM files and creates the .bai index files.

Author(s)

Michael Lawrence

See Also

gsnap

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.