DrImpute {DrImpute} | R Documentation |
Imputing dropout events in single-cell RNA-sequencing data.
DrImpute(X, ks = 10:15, dists = c("spearman", "pearson"), method = "mean", cls = NULL, seed = 1, zerop = 0)
X |
Gene expression matrix (gene by cell). |
ks |
Number of cell clustering groups. Default set to ks = 10:15. |
dists |
Distribution matrices to use. Default is set to c("spearman", "pearson"). "eucleadian" can be added as well. |
method |
Use "mean" for mean imputation, "med" for median imputation. |
cls |
User can manually provide clustering information. Using different base clusterings. each row represent different clusterings. each column represent each cell. |
seed |
User can provide a seed. |
zerop |
zero percentage of resulting imputation is at least zerop. |
Imputed Gene expression matrix (gene by cell).
Il-Youp Kwak
Il-Youp Kwak, Wuming Gong, Kaoko Koyano-Nakagawa and Daniel J. Garry (2017+) DrImpute: Imputing dropout eveents in single cell RNA sequencing data
data(exdata) exdata <- preprocessSC(exdata) exdata <- exdata[1:3000, 1:80] logdat <- log(exdata+1) cls <- getCls(logdat) logdat_imp <- DrImpute(logdat, cls = cls)