GeneSelector {GeneSelector}R Documentation

Exclude genes from being candidates for differential expression

Description

GeneRankings and AggregatedRankings from several statistics are unified. According to a user-defined or adaptively determined threshold via multiple testing procedures, all genes are checked whether they fall below this threshold consistenly in all statistics used. If this criterion is not met, then the gene is selected.
A final order of the genes is defined by the following criteria

1.
A user-defined ranking of the used statistics, i.e. the user decides which statistic is most important
2.
'Selection', i.e. falling below the threshold yes/no
3.
The obtained ranks. The rank from the most important statistic is considered, then that from the second most important, and so on.

Usage

GeneSelector(Rlist, ind = NULL, indstatistic = 1:length(Rlist), 
            threshold = c("user", "BH", "qvalue", "Bonferroni", "Holm", 
            "Hochberg", "SidakSS", "SidakSD", "BY"), 
            maxrank = NULL, maxpval = 0.05)

Arguments

Rlist A list of objects of class RepeatedRanking or AggregatedRanking, all based on the same data.
ind Indices of genes to be considered. Defaults to all.
indstatistic An index vector defining the importance of the elements of Rlist (typically this is the importance of the used statistics). For instance, if RList consists of five elements, then indstatistic=c(2,4,1,3,5) would give most importance to the second statistic.
threshold How the threshold is determined. Can be either "user" (then the threshold is specified via maxrank) or a multiple testing procedure (s. AdjustPvalues). In this case, the p-values of that element of Rlist attributed most importance (s. indtstatistic) are adjusted and the number of p-values falling below maxpval is used as threshold rank. If the most important statistic provides no p-values, then the ones of the second most are used (if available), and so on.
maxrank Specified if threshold="user". A positive integer that is regarded as threshold rank.
maxpval Specified if threshold is not user

Value

An object of class CombinedRanking.

Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

See Also

GeneRanking, AggregatedRanking

Examples

## Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### gene expression
xx <- toydata[-1,]
### Get Rankings from five different statistics
ordinaryT <- RankingTstat(xx, yy, type="unpaired")
baldilongT <- RankingBaldiLong(xx, yy, type="unpaired")
samT <- RankingSam(xx, yy, type="unpaired")
wilc <- RankingWilcoxon(xx, yy, type="unpaired")
wilcebam <- RankingWilcEbam(xx, yy, type="unpaired")
### form a list
LL <- list(ordinaryT, baldilongT, samT, wilc, wilcebam)
### order statistics (assign importance)
ordstat <-  c(3,4,2,1,5)
### start GeneSelector, threshold set to rank 50
gk50 <- GeneSelector(LL, indstatistic=ordstat, maxrank=50)
### start GeneSelector, using adaptive threshold based on p-values,
### here using the multiple testing procedure of Hochberg
gkpval <- GeneSelector(LL, indstatistic=ordstat, threshold = "BH", maxpval=0.05)
### show results
show(gkpval)
str(gkpval)
toplist(gkpval)
### which genes have been selected ?
SelectedGenes(gkpval)
### relative distance plot
plot(gkpval, top=5)
### Detailed information about gene 4
GeneInfoScreen(gkpval, which=4)

[Package GeneSelector version 1.2.0 Index]