tni.preprocess {RTN} | R Documentation

## A preprocessing function for objects of class TNI.

### Description

This is a generic function, provides all preprocessing methods for the 'tni.constructor' function.

### Usage

    tni.preprocess(object, rowAnnotation=NULL, colAnnotation=NULL, cvfilter=FALSE,
    verbose=TRUE)

### Arguments

`object` | this argument is an object of class `TNI-class`.
`rowAnnotation` | an optional data frame with gene annotation. Column 1 must provide all ids listed in the gene expression matrix. Ideally, col1 = <ID>, 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 `AVS-class` methods, it should also include chromosome coordinates: columns <CHROM>, <START> and <END>. Values in <CHROM> should be listed in [chr1, chr2, chr3, ..., chrX], while <START> and <END> correspond to chromosome positions (see `avs.evse`).
`colAnnotation` | an optional data frame with sample annotation.
`cvfilter` | a single logical value specifying to remove duplicated genes in the gene expression matrix using the gene annotation. In this case, 'rowAnnotation' must be provided, with col1 = <ID> and col2 = <GENEID>. Genes duplicated in col2 will be collapsed; the decision is made based on the maximum dinamic range (i.e. keeping the gene 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).

### Author(s)

Mauro Castro

### See Also

`TNI-class`

### Examples

    ## see 'tni.constructor'!

[Package RTN version 2.10.1 Index]