Package to perform a GSAfisher test for a gene-set analysis
This package could be downloaded and istalled: ```{r,message=FALSE} install.packages("GSAFisherComb_1.0.tar.gz") library(GSAFisherComb)
Or, as it is in Git Hub:
```{r,eval=FALSE}
library(devtools)
install_git("https://github.com/Merguerrero/GSAFisherComb")
To perform the test an object of class GSAfisher
or GSAfisher.mult
. In this package there is test data that you can load and try this functions. As we are working with pvalues, this functions accept as input a vector, a list of vectors or a matrix.
data("pvales.totest")
pvales.totest[1:20]
GSA_vector<-loadGSAfisher(pvales.totest)
GSA_vector
Load list of vectors:
data("pvales.mult")
GSA_list<-loadGSAfisher(pvales.mult)
Load matrix:
data("pvales.matrix")
GSA_matrix<-loadGSAfisher(pvales.matrix)
Once the data is loaded, with the function GSAfisher
the test is done. The output of the test differ with the class of the data.
res.Gsa<-GSAfisher(GSA_vector)
res.Gsa
For lists:
res.Gsa.list<-GSAfisher(GSA_list)
res.Gsa.list
For matrix:
res.Gsa.matrix<-GSAfisher(GSA_matrix)
res.Gsa.matrix
To see the result of the test in a ordered way the function summary prints some information:
summary(res.Gsa)
To see if the result of the GSAfisher
of the class GSAfisher.mult follows a chisquare distribution.
plot(res.Gsa.list)
If we are interested in the distribution of the result, an histogram with the density can also be plotted.
hist(res.Gsa.matrix)
This project is licensed under the GPL 3.0 License - see the LICENSE.md file for details
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