RTN (version 1.10.0)

tni.preprocess: A preprocessing function for objects of class TNI.

Description

This is a generic function.

Usage

tni.preprocess(object, gexpIDs=NULL, cvfilter=TRUE, verbose=TRUE)

Arguments

object

an object. When this function is implemented as the S4 method of class TNI-class, this argument is an object of class 'TNI'.

gexpIDs

an optional data frame or matrix with probe-to-gene annotation. Column 1 must provide all probe ids listed in the 'gexp' matrix. Ideally, col1 = , col2 = , and col3 = . 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 , and . Values in should be listed in [chr1, chr2, chr3, ..., chrX], while and correspond to chromosome positions (see avs.evse).

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 = and col2 = . 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).

See Also

TNI-class

Examples

data(dt4rtn)

rtni <- new("TNI", gexp=dt4rtn$gexp, transcriptionFactors=dt4rtn$tfs)
rtni <- tni.preprocess(rtni,gexpIDs=dt4rtn$gexpIDs)