knitr::opts_chunk$set( echo=TRUE, warning=FALSE, message=FALSE, error=FALSE) #, dpi=150)
Suppose we wanted to add a new GSEA method named superGSEA
to the methods that
the seas()
function can delegate to via its methods
argument, we need to add
the following internal sparrow methods.
validate.inputs.superGSEA
: Choose either .validate.inputs.full.design
or
.validate.inputs.preranked
depending on whether or not the method needs:.validate.inputs.full.design
;.validate.inputs.preranked
validate.x.superGSEA
: this is redundant, just put validate.X
. This will
be fixed in a future releasedo.superGSEA
: this method should take the parameters listed below, and
return the result of the superGSEA
call unmodified from its original
form that the superGSEA
method that is being wrapped returns it. The
parameters of the do.superGSEA
function are:gsd
: the pre-conformed GeneSetDb
x
: the expression matrix or pre-ranked stats vectordesign
: the design matrix. If the method uses a pre-ranked stats vector
just ignore this argument in the do.superGSEA
function body.contrast
: the contrast to test. If the method uses a pre-ranked stats
vector just ignore this argument in the do.superGSEA
function body.gsd.idxs
: this will be a list of gene sets. The names are the
collection;;name
tuples pasted together, and the values are integers
indices into the rows of x
for each gene in the gene set. Genes in
the gene set that are not in x
have already been removed.superGSEA
when the default values are not what you want....
: any other formal arguments defined in superGSEA
will be passed
into here, and it will be your responsibility to extract them and pass
them down into the superGSEA
call.mgres.superGSEA
: The function takes the output from do.superGSEA
and
turns it into a data.table
that minimally has collection
, name
,
pval
, and padj
columns.Look to the implementation in the do.camera.R
file for a reference.
Session Information
sessionInfo()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.