ITALICSTrain: ITALICS training

In ITALICS: ITALICS

Description

Estimation of the quartet effect based on several normal sample chips

Usage

trainITALICS (dir,  amplicon=2.1, deletion=-3.5, deltaN=0.15, forceGL=c(-0.2,0.2), param=c(d=2), nbsigma=1, ...)

Arguments

dir	The directory containing the normal sample chips. All theses chips should be of the same type hind, xba, nsp or sty. Only .CEL files be considered
amplicon	see the amplicon parameter in the daglad function
deletion	see the deletion parameter in the daglad function
deltaN	see the deltaN parameter in the daglad function
forceGL	see the forceGL parameter in the daglad function
param	see the param parameter in the daglad function
nbsigma	see the nbsigma parameter in the daglad function
...	Other daglad parameters.

Details

The ITALICS function take into account a quartet effect which is computed on a reference data set of normal women samples. The ITALICSData provide quartetEffect for the Xba, Hind, Sty and Nsp chip computed on our own reference data set.

We recommand that you use your own reference data set to compute the quartet Effect by using the trainITALICS function. ITALICS reference data should contain only woman normal samples. Furthermore we recommand that you check that none of these chip have obvious spatial artifact. To so read the cel files using the read.affybatch (form the affy package). Then use the image function on the obtain affybatch object.

Value

a data.frame with two column fsetid and quartetEffect

Note

People interested in tools dealing with array CGH analysis and DNA copy number analysis can visit our web-page http://bioinfo.curie.fr.

Author(s)

Guillem Rigaill, [e-mail].

Source

Institut Curie, [e-mail].

ITALICS documentation built on Nov. 8, 2020, 6:48 p.m.