Usage
get.network(data.obj, p.or.q = 0.05,
standardized = TRUE, min.std.effect = 0,
collapse.linked.markers = TRUE, verbose = FALSE,
plot.linkage.blocks = FALSE, threshold.power = 1)
Arguments
p.or.q
A numerical threshold indicating the maximum adjusted p value considered significant. If an fdr method has been used to correct for multiple testing, this value specifies the maximum q value considered significant. standardized
A logical value indicating whether values placed in weighted adjacency matrix are standardized values or unstandardized values.
min.std.effect
A numerical threshold indicating the absolute value of the minimum standard effect size to be shown in the plot. The default value of 0 performs no thresholding.
collapse.linked.markers
A logical value. If TRUE markers are combined into linkage blocks based on correlation. If FALSE, each marker is treated as an independent observation.
verbose
A logical value indicating whether the function progress should be printed to the screen.
plot.linkage.blocks
A logical value indicating whether the chromosomes should be plotted with their linkage blocks delineated. The type of plot produced differs depending on which choice is specified by linkage.method.
threshold.power
The linkage blocks are calculated by finding communities in a correlation matrix of genetic markers. This power indicates a soft-thresholding power for the correlation matrix. The higher the power, the more blocks will be generated.