imputeByCells: Imputation based on cell-to-cell relationships

In zky0708/2DImpute: 2DImpute: Imputing scRNA-seq data from correlations in both dimensions

Description

This function imputes dropout-suspected zeros by borrowing information from similar cells using k-nearest neighbors (kNN) regression.

Usage

imputeByCells(exprs, dropout_ind, k = 10, ncores = 1, verbose = TRUE)

Arguments

exprs	A log-transformed expression matrix, where rows and columns corresponds to genes and cells, respectively.
dropout_ind	A matrix where each row contains the indices of zero entries (first column for gene name, second column for cell ID) that are suspected as dropouts.
k	Number of neighbors to be used in the kNN regression. Default is 10.
ncores	Number of cores to use. Default is 1.
verbose	Whether to show the progress of imputation. Default is TRUE.

Value

An imputed version of gene expression matrix.

zky0708/2DImpute documentation built on March 12, 2020, 3:13 a.m.