This class describes objects to handle data values and information about genes and samples used in the data. Here, it is possible to put any field from data tables that you want.
This class of objects is intended to define an intermediate step
between the external world (data tables, gene groups, gene networks,
etc) and real raw objects given by the class
maigesRaw. In this intermediate step the user can do any
type of exploratory analysis and set bad spots (at slot
BadSpots), or to do any type of calculation they judge
important in the fields of
This class of objects is created by a call from
loadData. The functions
addPaths may also be used to add information for gene
groups and gene networks. After the exploratory analysis it must be
converted in an object of class
maigesRaw using the
If you have the package Rgraphviz installed and working it is
possible to display the graphs stored in the slot
contains a list with matrices. Each matrix has
nrow = number of spots and
ncol = number of data
tables (or chips) with the numerical values of each data field
specified by the user in the configuration file used as parameter
a list containing character vectors. These vectors specify genes from the gene groups that must be studied. Each vector is used as a gene group. The names of the groups are catch from the names of the vectors from the list, that is catch from file names.
specifying gene regulatory networks (or pathways). As in the
previous slot, the names are catch from file names and stored as
names of the elements from the list.
a list containing the number of rows (
gridC) of grids, the number of rows (
and columns (
spotC) of spots inside each grid and the total
number of spots.
data frame giving the gene labels. These labels are generally used during the data analysis.
data frame giving the sample labels. These labels are generally used during the data analysis.
logical vector specifying spots that was judged as bad ones. By default this slot is created as a vector of FALSEs with same length as number of spots.
char string that receives any comment about the dataset. The dataset description is stored in this slot.
char string giving the date and hour that the object was created.
list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.
signature(x = 'maigesPreRaw'): print method for
signature(x = 'maigesPreRaw'): show method for
signature(x = 'maigesPreRaw'): summary method for
Gustavo H. Esteves <email@example.com>
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