tni.preprocess {RTN} | R Documentation |
This is a generic function, provides all preprocessing methods for the 'tni.constructor' function.
tni.preprocess(object, rowAnnotation=NULL, colAnnotation=NULL, cvfilter=TRUE, verbose=TRUE, gexpIDs)
object |
this argument is an object of class |
rowAnnotation |
an optional data frame or matrix with probe-to-gene annotation (e.g. probe-to-gene information). Column 1 must provide all probe ids listed in the 'gexp' matrix. Ideally, col1 = <PROBEID>, col2 = <GENEID>, and col3 = <SYMBOL>. Additional annotation can be included in the data frame and will be passed to the resulting TNI object. Furthermore, in order to eventually use the TNI object in |
colAnnotation |
This option has not yet been implemented! |
cvfilter |
a single logical value specifying to remove duplicated genes in the gene expression matrix using the probe-to-gene annotation. In this case, 'gexpIDs' must be provided, with col1 = <PROBEID> and col2 = <GENEID>. The decision is made based on the maximum dinamic range (i.e. keeping the probes with max coefficient of variation across all samples). |
verbose |
a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE). |
gexpIDs |
deprected argument! please use 'rowAnnotation'. |
Mauro Castro
## see 'tni.constructor'!