Description Usage Arguments Value Note Author(s) Examples
assign expression data sample(s) to CIT Colon Cancer Molecular Subtype(s)
1 2 3 4 5 6 7 8 9 10 11 | cit.assignCcmst( data,
data.annot,
data.colId="Probe.Set.ID",
data.colMap=c("Probe.Set.ID","Gene.Symbol","Ensembl","UniGene.ID")[1],
citccmst.annot=NULL,citccmst.colId="Probe.Set.ID",
citccmst.colMap=c("Probe.Set.ID","Gene.Symbol","Ensembl","UniGene.ID")[1],
dist.method="dqda",
dist.difftopcentcutoff=NULL,
dist.disttocentcutoff=NULL,
dist.maxcutoff=NULL,
plot=FALSE)
|
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 |
citccmst.annot |
affymetrix annotation data.frame, if NULL (default) take the embedded annotation in object citccmst$data.annot |
citccmst.colId |
name of the column in citccmst.annot corresponding to rownames of citccmst$data. Default "Probe.Set.ID" |
citccmst.colMap |
name of the column in citccmst.annot containing the same annotation as in data.colMap |
dist.method |
metric to compute distance to assign a sample to a subtype ("pearson", "dlda", "dqda","euclidian"). Default "dqda". |
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 citccmst.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 |
dist.maxcutoff |
samples for which nearest centroid is above this threshold are discarded (used only if |
plot |
if TRUE plot an acp of cit data used to classify, and of the input data with subtype affectation and dist to centroid class |
a data.frame with 4 columns : "citccmst" assignments to the closest of the 6 subtype centroids, "citccmst.mixed" assignment to the n closest subtypes depending on dist.difftopcentcutoff, "citccmst.core" assignments without outlier and mixed samples and citccmst.confidence a confidence assignment annotation (CORE, MIXED or OUTLIER)
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 CITR@ligue-cancer.net
Laetitia Marisa
1 2 3 4 5 6 7 8 9 10 11 12 | #load(list.files(system.file("extdata", package="citccmst"), full.names=TRUE))
##load citvalid.exp.norm object
#citvalid.exp.annot <- data.frame(id=rownames(citvalid.exp.norm), stringsAsFactors=FALSE,
# row.names=rownames(citvalid.exp.norm) )
#citccmst <- cit.assignCcmst( data=citvalid.exp.norm,
# data.annot=citvalid.exp.annot,
# data.colId="id",
# data.colMap="id" ,
# citccmst.colMap="Probe.Set.ID",
# plot=TRUE
# )
#head(citccmst)
|
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