getPatterns | R Documentation |
Given the M1 predicted expression profiles of differentially expressed genes in a transition, the function uses PAM clustering to divide differentially expressed genes into clusters (patterns)
getPatterns(
expr,
do.zscore = T,
c.method = "pam",
k = NULL,
d.method = function(x) as.dist((1 - cor(t(x)))/2),
do.plot = T,
plot.filename = NULL
)
expr |
The M1 predicted expression profiles of differentially expressed genes in a transition |
do.zscore |
If TRUE, perform gene based zscore transformation prior to clustering |
c.method |
The algorithm to find pattern clusters, currently support "pam" and "kmeans" |
k |
The number of patterns to be discovered; if NULL, gap statistic (cluster::clusGap) will be used to determine an optimal k; parameters of cluster::clusGap are set as follows: k.max=10, B=50 |
d.method |
The distance method |
do.plot |
Whether to plot discovered patterns |
plot.filename |
The file name of the plot; if NULL, plot to the screen |
An object of class "pam" or "kmeans" representing the clustering results.
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