View source: R/func__networkAnalyser__allelicCoMatrix.R
allelicCoMatrix | R Documentation |
Create a co-occurrence matrix from allelic PAM
allelicCoMatrix( clusters = NULL, pam = NULL, hclust.method = NULL, hclust.dist = "binary" )
clusters |
A named or unnamed list of allele name vectors that define alleles of each cluster. Every vector must contain at least two alleles. |
pam |
An allelic presence-absence matrix, where 1 denotes presence of an allele and 0 denotes absence of an allele. |
hclust.method |
Method for clustering columns in the output co-occurrence matrix. Default: NULL (no clustering) |
hclust.dist |
Distance metric used for column-wise clustering. Default: binary. |
A list of elements: m, a co-occurrence matrix; c, clusters, recordered if hclust.method != NULL; g: a vector (method, dist) for arguments of column-wise clustering (grouping).
hclust.method and hclust.dist are passed to R base functions hclust and dist as arguments.
Yu Wan (wanyuac@126.com)
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