Description Usage Arguments Details Value Examples
View source: R/accessClass_pcOut.R
Given an object of class aespcOut
or superpcOut
,
as returned by the functions AESPCA_pVals
or
SuperPCA_pVals
, respectively, and the name or unique ID of
a pathway, return a data frame of the principal components and a data
frame of the loading vectors corresponding to that pathway.
1 2 3 4 5 6 7 | getPathPCLs(pcOut, pathway_char, ...)
## S3 method for class 'superpcOut'
getPathPCLs(pcOut, pathway_char, ...)
## S3 method for class 'aespcOut'
getPathPCLs(pcOut, pathway_char, ...)
|
pcOut |
An object of classes |
pathway_char |
A character string of the name or unique identifier of a pathway |
... |
Dots for additional arguments (currently unused). |
Match the supplied pathway character string to either the
pathways
or terms
columns of the pVals_df
data frame
within the pcOut
object. Then, subset the loadings_ls
and
PCs_ls
lists for their entries which match the supplied pathway.
Finally, return a list of the PCs, loadings, and the pathway ID and name.
A list of four elements:
PCs
: A data frame of the principal components
Loadings
: A matrix of the loading vectors with features
in the row names
pathway
: The unique pathway identifier for the
pcOut
object
term
: The name of the pathway
NULL
NULL
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ### Load Data ###
data("colonSurv_df")
data("colon_pathwayCollection")
### Create -Omics Container ###
colon_Omics <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection,
response = colonSurv_df[, 1:3],
respType = "survival"
)
### Calculate Supervised PCA Pathway p-Values ###
colon_superpc <- SuperPCA_pVals(
colon_Omics,
numPCs = 2,
parallel = TRUE,
numCores = 2,
adjustment = "BH"
)
### Extract PCs and Loadings ###
getPathPCLs(
colon_superpc,
"KEGG_PENTOSE_PHOSPHATE_PATHWAY"
)
|
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