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

Description Usage Arguments Value Examples

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

1
2
3
4
5
6
7
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
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)

rqt documentation built on Nov. 8, 2020, 4:50 p.m.