rqt-geneTestMeta: This function performs a gene-level meta-analysis based on...

In izhbannikov/rqt: rqt: utilities for gene-level meta-analysis

This function performs a gene-level meta-analysis based on combined effect sizes.

Description

This function performs a gene-level meta-analysis based on combined effect sizes.

This function performs a gene-level meta-analysis based on combined effect sizes.

Usage

geneTestMeta(objects, ...)

## S4 method for signature 'list'
geneTestMeta(
  objects,
  perm = 0,
  STT = 0.2,
  weight = FALSE,
  cumvar.threshold = 75,
  out.type = "D",
  method = "pca",
  scaleData = FALSE,
  asym.pval = FALSE,
  comb.test = "wilkinson",
  penalty = 0.001,
  verbose = FALSE
)

Arguments

objects	List of objects of class rqt
...	Additional parameters to pass to the function
perm	Integer indicating the number of permutations to compute p-values. Default: 0.
STT	Numeric indicating soft truncation threshold (STT) to convert to gamma parameter (must be <= 0.4). Needed for an optimal parameter a in Gamma-distribution. Default: 0.2. See, for example, Fridley, et al 2013: "Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study".
weight	Logical value. Indicates using weights (see Lee et al 2016). Default: FALSE.
cumvar.threshold	Numeric value indicating the explained variance threshold for PCA-like methods. Default: 75
out.type	Character, indicating a type of phenotype. Possible values: D (dichotomous or binary), C (continous or quantitative).
method	Method used to reduce multicollinerity and account for LD. Default: pca. Another methods available: lasso, ridge, pls.
scaleData	A logic parameter (TRUE/FALSE) indicating scaling of the genotype dataset.
asym.pval	Indicates Monte Carlo approximation for p-values. Default: FALSE.
comb.test	Statistical test for combining p-values.
penalty	Value of penalty parameter for LASSO/ridge regression. Default: 0.001
verbose	Indicates verbosing output. Default: FALSE.

Value

A list of two: (i) final.pvalue - a final p-value across all studies; (ii) pvalueList - p-values for each study;

A list of two: (i) final.pvalue - a final p-value across all studies; (ii) pvalueList - p-values for each study;

Examples

data1 <- data.matrix(read.table(system.file("extdata/phengen2.dat",
                                           package="rqt"), skip=1))
pheno <- data1[,1]
geno <- data1[, 2:dim(data1)[2]]
colnames(geno) <- paste(seq(1, dim(geno)[2]))
geno.obj <- SummarizedExperiment(geno)
obj1 <- rqt(phenotype=pheno, genotype=geno.obj)

data2 <- data.matrix(read.table(system.file("extdata/phengen3.dat",
                                           package="rqt"), skip=1))
pheno <- data2[,1]
geno <- data2[, 2:dim(data2)[2]]
colnames(geno) <- paste(seq(1, dim(geno)[2]))
geno.obj <- SummarizedExperiment(geno)
obj2 <- rqt(phenotype=pheno, genotype=geno.obj)

data3 <- data.matrix(read.table(system.file("extdata/phengen.dat",
                                           package="rqt"), skip=1))
pheno <- data3[,1]
geno <- data3[, 2:dim(data3)[2]]
colnames(geno) <- paste(seq(1, dim(geno)[2]))
geno.obj <- SummarizedExperiment(geno)
obj3 <- rqt(phenotype=pheno, genotype=geno.obj)

res.meta <- geneTestMeta(list(obj1, obj2, obj3))
print(res.meta)

izhbannikov/rqt documentation built on Aug. 2, 2024, 1:39 p.m.