Description Usage Arguments Details Value Author(s) Examples
An improved version for RRHO, which aims to correct the intepretation for top left region (up in x and down in y) nad bottom right region.
1 2 |
list1 |
data.frame. First column is the element (possibly gene) identifier, and the second is its value on which to sort. For differential gene expression, values are often -log10(P-value) * sign(effect). |
list2 |
data.frame. Same as list1. |
stepsize |
Controls the resolution of the test: how many items between any two overlap tests. |
labels |
Character vector with two elements: the labels of the two lists. |
plots |
Logical. Should output plots be returned? |
outputdir |
Path name where plots ae returned. |
BY |
Logical. Should Benjamini-Yekutieli FDR corrected pvalues be computed? |
log10.ind |
Logical. Should pvalues be reported and plotted in -log10 scale and not -log scale? |
We improved the algorithm such that all four regions of RRHO plot are meaningful
list of result
hypermat |
Matrix of -log(pvals) of the test for the first i,j elements of the lists. |
Caleb
1 2 3 4 5 6 7 8 9 10 | plotFolder <- 'plot'
system(paste('mkdir -p', plotFolder))
list.length <- 100
list.names <- paste('Gene',1:list.length, sep='')
set.seed(15213)
gene.list1<- data.frame(list.names, sample(100)*sample(c(1,-1),100,replace=TRUE))
gene.list2<- data.frame(list.names, sample(100)*sample(c(1,-1),100,replace=TRUE))
# Enrichment alternative
RRHO.example <- RRHO2(gene.list1, gene.list2,
labels=c('x','y'), plots=TRUE, outputdir=plotFolder, BY=TRUE, log10.ind=TRUE)
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