scimpute: use scImpute to impute dropout values in scRNA-seq data

In Vivianstats/scImpute: Accurate and robust imputation of single-cell RNA sequencing data

Description

use scImpute to impute dropout values in scRNA-seq data

Usage

scimpute(count_path, infile = "csv", outfile = "csv", type = "count",
  out_dir, labeled = FALSE, drop_thre = 0.5, Kcluster = NULL,
  labels = NULL, genelen = NULL, ncores = 5)

Arguments

count_path	A character specifying the full path of the raw count matrix;
infile	A character specifying the type of file storing the raw count matrix; can be "csv", "txt", or "rds". The input file shoule have rows representing genes and columns representing cells, with its first row as cell names and first column as gene names.
outfile	A character specifying the type of file storing the imputed count matrix; can be "csv", "txt", or "rds".
type	A character specifying the type of values in the expression matrix. Can be "count" (default) or "TPM".
out_dir	A character specifying the full path of the output directory, which is used to store all intermdediate and final outputs.
labeled	A logical value indicating whether cell type information is available. labels must be specified if labeled = TRUE.
drop_thre	A number between 0 and 1, specifying the threshold to determine dropout values.
Kcluster	An integer specifying the number of cell subpopulations. This parameter can be determined based on prior knowledge or clustering of raw data. Kcluster is used to determine the candidate neighbors of each cell.
labels	A character vector specifying the cell type of each column in the raw count matrix. Only needed when labeled = TRUE. Each cell type should have at least two cells for imputation.
genelen	An integer vector giving the length of each gene. Order must match the gene orders in the expression matrix. genelen must be specified if type = "count".
ncores	A integer specifying the number of cores used for parallel computation.

Value

scImpute returns a vector giving the column indices of outlier cells. It saves the imputed count matrix to scimpute_count.csv, scimpute_count.txt, or scimpute_count.rds (depending on outfile) to out_dir.

Author(s)

Wei Vivian Li, [e-mail]

Jingyi Jessica Li, [e-mail]

References

Li, W. V., & Li, J. J. (2018). An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nature Communications, 9(1), 997.

Vivianstats/scImpute documentation built on Aug. 21, 2019, 1:49 p.m.