ratio: Ratio Th between the observed features in common and the...

In sdef: Synthesizing List of Differentially Expressed Features

Description

The function for each experiment calculates the ratio T(h) for each threshold h, using the list of p-values or the other measure used in the experiment to rank the features, (e.g. posterior probability, correlation).

Usage

ratio(data, pvalue = TRUE, interval = 0.01,
name ="Distribution of T(h)",dir = getwd(),
dataname = "dataratio")

Arguments

data	Lists of pvalues to be compared
pvalue	Indicate if the data are pvalues (TRUE) or posterior probability (FALSE). If they are posterior probability they are transformed in pvalues. If correlation is used, select p-value=FALSE
interval	The interval between two threshold
name	The name to be used in the plots
dir	Directory for storing the plots
dataname	The name of the file containing the data (Pvalue)

Details

This function calculates the ratio T(h) of observed number of features in common between the lists vs the expected number under the hypothesis of independence for each threshold h. The expected numbers are calculated as the product among the marginals divided by (numbers of features)^(number of lists-1). T(hmax) identifies the maximum of the statistic T(h) and it is shown on the plot.

Value

Returns a plot with the distribution of T(h) showing where T(hmax) and hmax are located. The same plot is also saved in the directory specified by the user. It returns also an object of class list with the ratio, the thresholds and other attributes. In particular:

h	Threshold corresponding to T(h) values
DE	Differentially expressed features in each experiment
ratios	Vector or T(h) values for each threshold
Common	Features in common corresponding to the T(h) values
interval	Interval on the p-value scale defined by the user (default is 0.01)
name	Names to be used in the plots (defined by the user)
pvalue	Logical: TRUE if the measures used for the analysis are p-value, FALSE if they are posterior probabilities
dataname	The name of the file where the data has been saved

Author(s)

Alberto Cassese, Marta Blangiardo

References

Stone et al.(1988), Investigations of excess environmental risks around putative sources: statistical problems and a proposed test,Statistics in Medicine, 7, 649-660.

M.Blangiardo and S.Richardson (2007) Statistical tools for synthesizing lists of differentially expressed features in related experiments, Genome Biology, 8, R54.

Examples

data = simulation(n=500,GammaA=1,GammaB=1,r1=0.5,r2=0.8,
DEfirst=300,DEsecond=200,DEcommon=100)
Th<- ratio(data=data$Pval)

sdef documentation built on May 2, 2019, 8:55 a.m.