cit.centroids: cit.centroids

In citbcmst: CIT Breast Cancer Molecular SubTypes Prediction

Description

define centroids for a given partition of individuals (columns) and calculate distance between individuals and centroids

Usage

cit.centroids(  d,
classes,
rowCentering=c(NA,function(x)mean(x, na.rm=TRUE),function(x)median(x, na.rm=TRUE))[[3]],
rowClassesForAggregation=NULL,
rowClassesToKeep=NULL,
dist.meth=c("spearman","euclidian","maximum","manhattan",
"canberra","binary","minkowski","pearson","dlda","dqda"),
maxDist=0.5,
...)

Arguments

d	a data.frame of numeric data
classes	a vector defining a partition of data columns (NA values accepted)
rowCentering	NA: no row centering; otherwise: function to be used for row centering
rowClassesForAggregation	partition of the rows , used to aggregate rows from the same class (1 aggregated row per class will be calculated)
rowClassesToKeep	to restrict the centroid's calculation to the some aggregated rows (= row classes)
dist.meth	distance method used to calculate distance between individuals (columns in d) and centroids
maxDist	individuals for which nearest centroid is above this threshold are discarted (used only if dis.meth = "pearson" or "spearman")
...	parameters from cit.distToCentroids function

Value

a list with two objects : centroids and dist2Centroids

Note

This is a contribution from the Tumor Identity Cards (CIT) program founded by the 'Ligue Nationale Contre le Cancer' (France): http://cit.ligue-cancer.net. For any question please contact [e-mail]

Author(s)

Aurelien de Reynies

citbcmst documentation built on May 2, 2019, 6:03 a.m.