RNAseqNet (version 0.1.5)

chooseSigma: Select the threshold sigma for hd-MI.

Description

chooseSigma computes the average intra-donor pool variance for different values of sigma. It helps choosing a sigma that makes a good trade-off between homogeneity within the pool of donors and variety (large enough number of donors in every pool).

Usage

chooseSigma(X, Y, sigma_list, seed = NULL)

Value

a data frame with the values of sigma and the corresponding intra-donor pool variances

Arguments

X

n x p numeric matrix containing RNA-seq expression with missing rows (numeric matrix or data frame)

Y

auxiliary dataset (n' x q numeric matrix or data frame)

sigma_list

a sequence of increasing positive values for sigma (numeric vector)

seed

single value, interpreted as an in integer, used to initialize the random number generation state

Author

Alyssa Imbert, Nathalie Vialaneix,

Details

The average intra-donor pool variance is described in (Imbert et al., 2018).

References

Imbert, A., Valsesia, A., Le Gall, C., Armenise, C., Lefebvre, G. Gourraud, P.A., Viguerie, N. and Villa-Vialaneix, N. (2018) Multiple hot-deck imputation for network inference from RNA sequencing data. Bioinformatics. tools:::Rd_expr_doi("10.1093/bioinformatics/btx819").

See Also

varIntra

Examples

data(lung)
data(thyroid)
nobs <- nrow(lung)
miss_ind <- sample(1:nobs, round(0.2 * nobs), replace = FALSE)
lung[miss_ind, ] <- NA
lung <- na.omit(lung)
sigma_stats <- chooseSigma(lung, thyroid, 1:5)
if (FALSE) plot(sigma_stats, type = "b")