gls: Gene-level statistics

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Description

Functions to calculate the gene-level statistic, as used in the gls parameter of gsAnalysis. A gene-level statistic calculates a measure of correlation between the expression of a gene and the class labels.

Usage

gls.cor(dat, labs, method = "pearson")

gls.regression(dat, labs)

gls.foldChange(dat, labs, logMeasurements = TRUE)

gls.tStatistic(dat, labs, pValue = FALSE, alternative = "two.sided")

gls.moderateTStatistic(dat,labs)

gls.nBinomTest(dat, labs,
	returnValue = c("pval", "qval", "foldChange", "log2FoldChange"),
	dispersionMethod = "blind",
	dispersionSharingMode = "fit-only",
	dispersionFitType = "local")

Arguments

dat	A numeric matrix of gene expression values for all analyzed genes. Here, each row corresponds to one gene, and each column corresponds to one sample. The rows must be named with the gene names used in the gene sets.
labs	A vector of class labels for the samples in dat.
logMeasurements	For gls.foldChange, whether the values in dat are logarithmized (logMeasurements=TRUE) or not (logMeasurements=FALSE).
method	For gls.cor, the correlation method to be used (see cor).
pValue	For gls.tStatistic, this specifies whether the p-value (pValue=TRUE) or the test statistic (pValue=FALSE) of the t test should be returned.
alternative	For gls.tStatistic, this specifies the alternative of the t-test. See also t.test.
returnValue	For gls.nBinomTest, this determines the type of values values that should be returned. "pval" returns the raw p-values, "qval" returns the p-values adjusted by the FDR, "foldChange" returns the fold changes, and "log2FoldChange" returns the log2 fold changes. For more details, see results.
dispersionMethod	For gls.nBinomTest, this specifies how the empirical dispersion is computed (see estimateDispersions).
dispersionSharingMode	For gls.nBinomTest, this specifies which values should be used by results (fitted values or empirical values, see estimateDispersions for more details).
dispersionFitType	For gls.nBinomTest, this determines the method for fitting the dispersion-mean relation (see estimateDispersions).

Details

Standard functions for the calculation of gene-level statistics (to be used in an analysis pipeline defined by gsAnalysis):

• gls.cor: Calculates the correlation of the gene expression values to the class labels.

• gls.regression: Calculates the slope of a linear regression of the gene expression values and the class labels.

• gls.foldChange: Calculates the (standard or log2) fold change between the measurements for the two classes.

• gls.tStatistic: Calculates the p-value or the statistic of a two-sample t test for the measurements of the two classes

• gls.moderateTStatistic: Calculates the moderate t statistic for the measurements of the two classes

• gls.nBinomTest: Applies the negative binomial test for sequencing data based on the DESeq2 package to test for differences between two classes (see results).

Value

Each of these function returns a numeric vector of gene-level statistics (one entry per gene).

See Also

geneSetAnalysis, gsAnalysis, gss, transformation

GiANT documentation built on Oct. 23, 2020, 7:56 p.m.