【生信技能】基因分型Cluster：ConsensusClusterPlus包进行聚类分析

#聚类代码

maxK=9

results=ConsensusClusterPlus(data,

              maxK=maxK,

              reps=50,

              pItem=0.8,

              pFeature=1,

              title=workDir,

              clusterAlg="pam",

              distance="euclidean",

              seed=123456,

              plot="png")

Arguments-各个参数说明

d

data to be clustered; either a data matrix where columns=items/samples and rows are features. For example, a gene expression matrix of genes in rows and microarrays in columns, or ExpressionSet object, or a distance object (only for cases of no feature resampling)

maxK

integer value. maximum cluster number to evaluate.

reps

integer value. number of subsamples.

pItem

numerical value. proportion of items to sample.

pFeature

numerical value. proportion of features to sample.

clusterAlg

character value. cluster algorithm. 'hc' hierarchical (hclust), 'pam' for paritioning around medoids, 'km' for k-means upon data matrix, or a function that returns a clustering. See example and vignette for more details.

title

character value for output directory. Directory is created only if plot is not NULL or writeTable is TRUE. This title can be an abosulte or relative path.

innerLinkage

hierarchical linkage method for subsampling.

finalLinkage

hierarchical linkage method for consensus matrix.

distance

character value. 'pearson': (1 - Pearson correlation), 'spearman' (1 - Spearman correlation), 'euclidean', 'binary', 'maximum', 'canberra', 'minkowski" or custom distance function.

ml

optional. prior result, if supplied then only do graphics and tables.

tmyPal

optional character vector of colors for consensus matrix

seed

optional numerical value. sets random seed for reproducible results.

plot

character value. NULL - print to screen, 'pdf', 'png', 'pngBMP' for bitmap png, helpful for large datasets.

writeTable

logical value. TRUE - write ouput and log to csv.

weightsItem

optional numerical vector. weights to be used for sampling items.

weightsFeature

optional numerical vector. weights to be used for sampling features.

res

result of consensusClusterPlus.

verbose

boolean. If TRUE, print messages to the screen to indicate progress. This is useful for large datasets.

corUse

optional character value. specifies how to handle missing data in correlation distances 'everything','pairwise.complete.obs', 'complete.obs' see cor() for description.

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