ICE: ICE: Impute CircRNA Expression

In bioinformatist/ICE: ICE: Impute CircRNA Expression

Usage

ICE(train.circ, train.pcg, new.pcg, gene.index, method = "KNN", num = 100, ...)

Arguments

train.circ	training circRNA expression dataset, which should be a numeric matrix with row names indicating samples, and column names indicating circRNA IDs.
train.pcg	training protein coding dataset, which should be a numeric matrix with with row names indicating samples, and column names indicating protein coding gene IDs.
new.pcg	protein coding expression dataset to be used for prediction, which should be a numeric matrix with row names indicating samples, and column names indicating protein coding gene IDs.
gene.index	either gene name (character) or index (column number) of circRNA to be imputed.
method	method for imputation, either "RF" for random forests, "KNN" for K-nearest neighbor or "SVM" for support vector machines. Uses KNN by default.
num	number of informative protein coding genes to be used in constructing imputation model. Default is 100 genes.
...

Examples

data("mionco.circ")
data("mionco.pcg")
pred.circ <- ICE(train.pcg = mionco.pcg, train.circ = mionco.circ, new.pcg = mionco.pcg, gene.index = "hsa_circ_0000801")

bioinformatist/ICE documentation built on July 5, 2020, 12:20 a.m.