SEA {rSEA} | R Documentation |
SEA
Description
returns SEA chart (a data.frame) including the test results and estimates for the specified
feature-sets from pathlist
.
Usage
SEA(
pvalue,
featureIDs,
data,
pathlist,
select,
tdphat = TRUE,
selfcontained = TRUE,
competitive = TRUE,
thresh = NULL,
alpha = 0.05
)
Arguments
pvalue |
Vector of p-values. It can be the name of the covariate representing the Vector of
all raw p-values in the |
featureIDs |
Vector of feature IDs. It can be the name of the covariate representing the IDs in the
|
data |
Optional data frame or matrix containing the variables in |
pathlist |
A list containing pathways defined by |
select |
A vector. Number or names of pathways of interest from the |
tdphat |
Logical. If |
selfcontained |
Logical. If |
competitive |
Logical. If |
thresh |
A real number between 0 and 1. If specified, the competitive null hypothesis will be tested against this threshold for each pathway and the corresponding adj. p-value is returned |
alpha |
The type I error allowed for TDP bound. The default is 0.05. |
Value
A data.frame is returned including a list of pathways with corresponding TDP bound estimate, and if specified, TDP point estimate and adjusted p-values
Author(s)
Mitra Ebrahimpoor
References
Mitra Ebrahimpoor, Pietro Spitali, Kristina Hettne, Roula Tsonaka, Jelle Goeman, Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods, Briefings in Bioinformatics, , bbz074, https://doi.org/10.1093/bib/bbz074
See Also
Examples
## Not run:
##Generate a vector of pvalues for a toy example
set.seed(159)
m<- 100
pvalues <- runif(m,0,1)^5
featureIDs <- as.character(1:m)
# perform a self-contained test for all features
setTest(pvalues, featureIDs, testype = "selfcontained")
# create 3 random pathway of size 60, 20 and 45
randpathlist=list(A=as.character(c(sample(1:m, 60))),
B=as.character(c(sample(1:m, 20))),
C=as.character(c(sample(1:m, 45))))
# get the seachart for the whole pathlist
S1<-SEA(pvalues, featureIDs, pathlist=randpathlist)
S1
# get the seachart for only first two pathways of the randpathlist
S2<-SEA(pvalues, featureIDs, pathlist=randpathlist, select=1:2)
S2
#sort the list by competitve p-value and select top 2
topSEA(S2, by=Comp.adjP, descending = FALSE, n=2)
#make an enrichment plot based on TDP.estimated of pathways
plotSEA(S1,n=3)
## End(Not run)