View source: R/FateID_functions.R
impGenes | R Documentation |
This function extracts all genes with an importance value for classifying cells into a given target cluster exceeding a given threshold for at least one of the random forest iterationns.
impGenes(fb, tn, ithr = 0.02, zthr = 2)
fb |
fateBias object returned by the function |
tn |
name of a target cluster, i. e. concatenation of a |
ithr |
positive real number. Threshold for the required importance measure (mean decrease in accuracy of classification upon removal, see randomForest) to include a gene into the output as important feature for classying cells in |
zthr |
positive real number. Threshold for the required z-score of the importance measure (importance divided by the standard deviation of importance) to include a gene into the output as important feature for classying cells in |
The function returns a list of two elements.
d |
a data frame with mean importance values for all genes surviving the filtering by |
d |
a data frame with the standard deviation of importance values for all genes surviving the filtering by |
The function produces a heatmap of d
with hierarchical clustering of the rows using the function pheatmap
from the pheatmap package.
x <- intestine$x y <- intestine$y 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) k <- impGenes(fb,"t6",ithr=.02,zthr=2)
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