cit.distToCentroids: cit.distToCentroids

In citbcmst: CIT Breast Cancer Molecular SubTypes Prediction

Description

calculate distance between individuals and centroids; used in cit.centroids()

Usage

cit.distToCentroids(d,
centroids,
dist.meth=c("spearman","euclidian","maximum","manhattan",
"canberra","binary","minkowski","pearson","dlda","dqda"),
maxDist=0.5,
d.isPretreated=FALSE,
sdifftop=NULL,
sdisttocent=NULL,
verbose=FALSE)

Arguments

d	a data.frame of numeric data
centroids	object obtained via a call to cit.centroids() (see slot 'centroids')
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")
d.isPretreated	indicate wether d is pretreated (row aggregation, row centering)...for internal use
sdifftop	cut-off on the diffences between distances to centroids. If the distance is inferior to this cut-off for n centroids the sample is assigned to the n groups in the output variable predmixed. If NULL, the cut-off is defined as the 1st decile of the difference between the top 2 closest centroids on data used to compute centroids.
sdisttocent	cut-off on the mad (median absolute deviation) of distances to the centroid to define a sample as outlier. If the distance to the centroid of the assigned group is superior to sdisttocent*mad(distances of centroids samples to this centroid)
verbose	boolean if output should be displayed

Value

a list giving the distance between individuals and centroids and the predicted class for each individuals

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, Laetitia Marisa

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