Description Usage Arguments Details Value Examples
Given an Omics
object and the name of a pathway, return
the -omes in the assay and the response as a (tibble) data frame.
1 2 3 4 | SubsetPathwayData(object, pathName, ...)
## S4 method for signature 'OmicsPathway'
SubsetPathwayData(object, pathName, ...)
|
object |
An object of class |
pathName |
The name of a pathway contained in the pathway collection in the object. |
... |
Dots for additional internal arguments (currently unused). |
This function subsets the assay by the matching gene symbols or IDs in the specified pathway.
A data frame of the columns of the assay in the Omics
object
which are listed in the specified pathway, with a leading column for
sample IDs. If the Omics
object has response information, these
are also included as the first column(s) of the data frame, after the
sample IDs. If you have the suggested tidyverse
package suite
loaded, then this data frame will print as a tibble
.
Otherwise, it will print as a data frame.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data("colonSurv_df")
data("colon_pathwayCollection")
colon_Omics <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection,
response = colonSurv_df[, 1:3],
respType = "survival"
)
SubsetPathwayData(
colon_Omics,
"KEGG_RETINOL_METABOLISM"
)
|
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