ZKfiltering: Filter outlying samples based on the standardized...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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

Description

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.

Author(s)

Fabricio Almeida-Silva

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

Examples

data(zma.se)
filt_exp <- ZKfiltering(zma.se)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.