dbGetGeneRegulationRanking {maDB}R Documentation

Rank genes according to the number of comparisons they are regulated.

Description

This function can be used to generate a ranking list for genes that contains the number of comparisons (from a selected set of comparisons in the database) the gene was regulated (where regulation can be for example be defined as an M value bigger than 1 or smaller -1). The ranking can be restricted to a subset of genes and comparisons. Note that the comparisons have to be created in the database (from expresison values using the dbCalculateRegulations method). By default the function maps first the submitted ids to UniGene IDs and calcultates therefore the ranking for genes (not for, in the case of Affymetrix, probe sets), bevertheless by setting no.mapping.to.ug=TRUE this mapping to UniGene IDs will be skipped and the ranking will be performed id per id.

Usage

dbGetGeneRegulationRanking(con, ug = NULL, id = NULL, include.by.name = NULL, exclude.by.name = NULL, include.by.pk = NULL, exclude.by.pk = NULL, count.cols = NULL, write.info.file = TRUE, search.column = "exposure_time", no.mapping.to.ug = FALSE ,m.up= 1, m.down= -1, v = TRUE, chip=NULL)

Arguments

con The connection to the (maDB) database.
ug A set of UniGene identifiers. The annotation table has to be created if this option is used!
id A set of ids (eg Affymetrix probe set IDs or the IDs that were used as rownames in the EexprSet@exprs tables that were inserted into the database).
include.by.name The comparisons are joined to the samples table. So comparisons can be selected or using the include.by.pk attribute, or using the sample names of the samples that were used as textit{red} signal channels in the calculation of the regulation value (M = log2(R / G)).
exclude.by.name Samples that should be excluded.
include.by.pk The primary keys of the comparisons that should be included to create the ranking.
exclude.by.pk The primary keys of the comparisons that should be excluded (makes only sense when the include.by.name was used, and not all of the comparisons that share the same sample names should be included).
count.cols The entries (of the samples table) that should be used to count the regulation. For example if you have in your database samples with 6 hours, 8 hours and 24 hours exposure time and you want to count for each gene the number of comparisons with 6 and 8 hours where they were regulated and additionally the number of comparisons with 24 hours exposure time samples, submit count.cols=list(c("6h","8h"),c("24h")) and for the attribute search.col search.col="exposure_time".
write.info.file If true a file called “HL” with the current date and “Info.txt” will be saved in the current working directory which contains the information which comaprisons were used to generate the ranking.
search.column The column of the samples table that should be used to distinguish between different comparisons (see attribute count.cols).
no.mapping.to.ug If TRUE the ranking will be computed for each submitted id, if FALSE each id will be mapped to UniGene IDs, and those will then be used to count the regulations. Because of this mapping it is important, that the annotation table in the database holds the correct information (see dbUpdateAnnotation for more information).
m.up Genes that have an M value bigger than this value will be counted as regulated (up–regulated!), the default is 1.
m.down Genes that have an M value smaller than this value will be counted as down–regulated.
v If additional information (progress bar...) should be written to the console.
chip The chip or array type (eg hgu133plus2).

Details

coming soon...

Value

A table with the information about how many times a gene was regulated.

Author(s)

Johannes Rainer

See Also

dbUpdateAnnotation, publishToDB, dbCalculateRegulations


[Package maDB version 1.2.0 Index]