imirage: iMIRAGE: imputated miRNA Activity from Gene Expression

In aritronath/iMIRAGE: iMIRAGE: imputed miRNA activity from gene expression (Title Case)

Description

Function to impute miRNA expression profile from protein coding expression dataset

Usage

imirage(train_pcg, train_mir, my_pcg, gene_index, method = "KNN",
  num = 50, target = "none", ...)

Arguments

train_pcg	training protein coding dataset. a numeric matrix with with row names indicating samples, and column names indicating protein coding gene IDs.
train_mir	training miRNA expression dataset. a numeric matrix with row names indicating samples, and column names indicating miRNA IDs.
my_pcg	test protein coding expression dataset. 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 miRNA 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 50 genes.
target	"none" (default), "ts.pairs", or dataframe/matrix/list. this argument accepts character strings to indicate the use of all candidate genes as predictors ("none), or use built-in TargetScan miRNA-gene pairs ("ts.pairs"). also accepts a dataframe , matrix or list object containing a column with names of miRNA and a column with the names of target genes.
...	optional parameters that can be passed on to the machine-learning method: RF (randomForest), KNN (knn.reg) or SVM(svm)

Value

a numeric vector with imputed expression levels of the miRNA

Examples

data(iMIRAGE.datasets)
imirage(GA.pcg, GA.mir, HS.pcg, gene_index="hsa-let-7c", method="KNN", num=50)
imirage(GA.pcg, GA.mir, HS.pcg, gene_index=25, method="KNN", num=50)

aritronath/iMIRAGE documentation built on Dec. 29, 2019, 1:28 a.m.