Filter outlying samples based on the standardized connectivity (Zk) method

Filter outlying samples based on the standardized connectivity (Zk) method

Usage

ZKfiltering(exp, zk = -2, cor_method = "spearman")

Arguments

exp

A gene expression data frame with genes in row names and samples in column names or a `SummarizedExperiment` object.

zk

Standardized connectivity threshold. Default is -2.

cor_method

Correlation method. One of "pearson", "biweight" or "spearman". Default is "spearman".

Value

Filtered gene expression data frame or `SummarizedExperiment` object.

References

Oldham, M. C., Langfelder, P., & Horvath, S. (2012). Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease. BMC systems biology, 6(1), 1-18.

See also

adjacency

Author

Fabricio Almeida-Silva

Examples

data(zma.se)
filt_exp <- ZKfiltering(zma.se)
#> Number of removed samples: 1