Description Usage Arguments Value Examples
View source: R/RaceID3_StemID2_class.R
This is a plotting function for visualizing the output of the diffexpnb
function.
1 2 |
x |
output of the function |
pthr |
real number between 0 and 1. This number represents the p-value cutoff applied for displaying differentially expressed genes. Default value is 0.05. The parameter |
padj |
logical value. If |
lthr |
real number between 0 and Inf. Differentially expressed genes are displayed only for log2 fold-changes greater than |
mthr |
real number between -Inf and Inf. Differentially expressed genes are displayed only for log2 mean expression greater than |
Aname |
name of expression set |
Bname |
name of expression set |
show_names |
logical value. If |
None
1 2 3 4 5 6 7 8 9 10 11 12 13 | x <- intestine$x
y <- intestine$y
v <- intestine$v
tar <- c(6,9,13)
fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)
thr <- .3
A <- rownames(fb$probs)[fb$probs[,"t6"] > .3]
B <- rownames(fb$probs)[fb$probs[,"t13"] > .3]
de <- diffexpnb(v,A=A,B=B)
plotdiffgenesnb(de,pthr=.05)
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