citbcmst (version 1.0.4)

cit.assignBcmst: cit.assignBcmst

Description

assign expression data sample(s) to CIT Breast Cancer Molecular Subtypes

Usage

cit.assignBcmst(  data,
data.annot,
data.colId="Probe.Set.ID",
data.colMap=c("Probe.Set.ID","Gene.Symbol","Ensembl","UniGene.ID")[1],
citbcmst.annot=NULL,citbcmst.colId="Probe.Set.ID",
citbcmst.colMap=c("Probe.Set.ID","Gene.Symbol","Ensembl","UniGene.ID")[1],
dist.method="dlda",
dist.difftopcentcutoff=NULL,
dist.disttocentcutoff=NULL,
dist.maxcutoff=NULL,
plot=FALSE)

Arguments

data

a data.frame of expression data with id as rownames

data.annot

a data.frame of data probes annotations

data.colId

name of the column in data.annot containing data probes id

data.colMap

name of the column in data.annot containing data probes names to map

citbcmst.annot

affymetrix annotation data.frame, if NULL (default) takes the embeded annotation in object citbcmst$data.annot

citbcmst.colId

name of the column in citbcmst.annot corresponding to rownames of citbcmst$data. Default "Probe.Set.ID"

citbcmst.colMap

name of the column in citbcmst.annot containing the same annotation as in data.colMap

dist.method

metric to compute distance to assign a sample to a subtype. Default for Affymetrix data "dlda". For other platforms "pearson".

dist.difftopcentcutoff

cut-off on the differences between distances to centroids. If the distance is inferior to this cut-off for n centroids the sample is assigned to the n subtypes in the output variable citbcmst.mixed. 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.

dist.disttocentcutoff

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 subtype is superior to sdisttocent*mad(distances of centroids samples to this centroid)

dist.maxcutoff

samples for which nearest centroid is above this threshold are discarted (used only if dis.meth = "pearson" or "spearman")

plot

if TRUE plot an acp of citdata used to classify, and of the input data with subtype affectation and dist to centroid class

Value

Examples

# load exp.norm.bertheau07 object stored in /inst/extdata
exp.annot.bertheau07 <- data.frame(id=rownames(exp.norm.bertheau07), stringsAsFactors=FALSE,
row.names=rownames(exp.norm.bertheau07) )
citbcmst.bertheau07 <- cit.assignBcmst(    data=exp.norm.bertheau07,
                                           data.annot=exp.annot.bertheau07,
                                           data.colId="id",
                                           data.colMap="id" ,
                                           citbcmst.colMap="Probe.Set.ID",
                                           dist.method="dlda",
                                           plot=TRUE
                                 )