SuperPCA_pVals {pathwayPCA} | R Documentation |
Given a supervised OmicsPath
object (one of
OmicsSurv
, OmicsReg
, or OmicsCateg
), extract the
first k principal components (PCs) from each pathway-subset of the
-Omics assay design matrix, test their association with the response
matrix, and return a data frame of the adjusted p-values for each
pathway.
SuperPCA_pVals( object, n.threshold = 20, numPCs = 1, parallel = FALSE, numCores = NULL, adjustpValues = TRUE, adjustment = c("Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", "TSBH"), ... ) ## S4 method for signature 'OmicsPathway' SuperPCA_pVals( object, n.threshold = 20, numPCs = 1, parallel = FALSE, numCores = NULL, adjustpValues = TRUE, adjustment = c("Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", "TSBH"), ... )
object |
An object of superclass |
n.threshold |
The number of bins into which to split the feature scores
in the fit object returned internally by the |
numPCs |
The number of PCs to extract from each pathway. Defaults to 1. |
parallel |
Should the computation be completed in parallel? Defaults to
|
numCores |
If |
adjustpValues |
Should you adjust the p-values for multiple comparisons? Defaults to TRUE. |
adjustment |
Character vector of procedures. The returned data frame
will be sorted in ascending order by the first procedure in this vector,
with ties broken by the unadjusted p-value. If only one procedure is
selected, then it is necessarily the first procedure. See the documentation
for the |
... |
Dots for additional internal arguments. |
This is a wrapper function for the pathway_tScores
,
pathway_tControl
, OptimGumbelMixParams
,
GumbelMixpValues
, and TabulatepValues
functions.
Please see our Quickstart Guide for this package: https://gabrielodom.github.io/pathwayPCA/articles/Supplement1-Quickstart_Guide.html
A data frame with columns:
pathways
: The names of the pathways in the Omics*
object (given in object@trimPathwayCollection$pathways
.)
setsize
: The number of genes in each of the original
pathways (given in the object@trimPathwayCollection$setsize
object).
terms
: The pathway description, as given in the
object@trimPathwayCollection$TERMS
object.
rawp
: The unadjusted p-values of each pathway.
...
: Additional columns as specified through the
adjustment
argument.
The data frame will be sorted in ascending order by the method specified
first in the adjustment
argument. If adjustpValues = FALSE
,
then the data frame will be sorted by the raw p-values. 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.
CreateOmics
; TabulatepValues
;
pathway_tScores
; pathway_tControl
;
OptimGumbelMixParams
; GumbelMixpValues
;
clusterApply
### Load the Example Data ### data("colonSurv_df") data("colon_pathwayCollection") ### Create an OmicsSurv Object ### colon_OmicsSurv <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection, response = colonSurv_df[, 1:3], respType = "surv" ) ### Calculate Pathway p-Values ### colonSurv_superpc <- SuperPCA_pVals( object = colon_OmicsSurv, parallel = TRUE, numCores = 2, adjustpValues = TRUE, adjustment = c("Hoch", "SidakSD") )