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 2.8.5 Index]