View source: R/func__networkAnalyser__alleleClusterDistr.R
alleleClusterDistr | R Documentation |
This function generates a matrix for co-occurrence of all alleles of each cluster in a give collection of bacterial samples. This function is particularly useful in investigating the distribution of allele clusters (such as maximal cliques) in bacterial samples. It can be considered as a simplified version of function getClusterMemberCoocurrence.
alleleClusterDistr(cls, pam)
cls |
A data frame of two columns for cluster IDs (first column) and allele contents (the second column, comma-delimited). This data frame can be generated from the output of function summariseCliques. Each cluster must consist of at least two alleles. |
pam |
An uncentred presence-absence matrix for alleles in the data frame cls. This is a binary matrix, where 1 denotes presence and 0 denotes absence. |
An n-by-m matrix, where n is the sample size and m is the cluster number.
Yu Wan (wanyuac@126.com)
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