Les: Les

In les: Identifying Differential Effects in Tiling Microarray Data

Description

Constructs an object of class 'Les' and stores experimental tiling microarray data. This is the initial step for all further analysis with the 'les' package.

Usage

Les(pos, pval, chr)

Arguments

pos	Integer vector containing the probe positions.
pval	Numeric vector containing the p-values corresponding to 'pos'. It must be of the same length as 'pos'.
chr	Vector specifying the chromosome each probe in located on. If missing all probes are located on one chromosome (default: 'chr0'). If specified it must be of the same length as 'pos'. Internally it will be stored as a factor.

Details

This method gathers all data necessary for subsequent analysis, checks for valid inputs and stores it in an object of class 'Les'.

The data is checked for the following criteria: 'pos' and 'chr' must not contain any NAs. 'pval' may contain NAs but such probes (including corresponding 'pos' and 'chr') are discarded for subsequent computation since they contain no usable information. Please note that in such a case fewer probes are stored in the resulting object then were passed to 'Les'. In case of duplicate probe positions on one chromosome a warning is printed. This normally indicates that probes from both strands are present in the data.

After storing the experimental data with 'Les' in an object the variables containing the original data can be deleted from the workspace. All further steps of 'les' will get their data from this object. This can be useful in cases when memory usage is a critical factor.

Value

Object of class 'Les' with filled slots: pos, pval, chr

Author(s)

Julian Gehring

Maintainer: Julian Gehring <[e-mail]>

See Also

Package: les-package

Class: Les

Methods and functions: Les estimate threshold regions ci chi2 export plot

Examples

data(spikeInStat)

x <- Les(pos, pval)
x

les documentation built on Nov. 8, 2020, 5:17 p.m.